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Conserved domains on  [gi|2462586280|ref|XP_054200810|]
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RNA-binding protein 6 isoform X2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM2_RBM6 cd12563
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup ...
 654-740 6.08e-50

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


:

Pssm-ID: 409979 [Multi-domain]  Cd Length: 87  Bit Score: 170.80  E-value: 6.08e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  654 ESKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMV 733
Cdd:cd12563      1 DSKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNKTGPMGHTYGFIDLDSHAEALRLVKLLQNLDPPLYIDGRRV 80


                   ....*..
gi 2462586280  734 AVNLATG 740
Cdd:cd12563     81 YVNVATG 87
RRM1_RBM6 cd12314
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This ...
 456-533 6.52e-46

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


:

Pssm-ID: 409753 [Multi-domain]  Cd Length: 78  Bit Score: 158.89  E-value: 6.52e-46
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462586280  456 RLIRLSGVPEDATKEEILNAFRTPDGMPVKNLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIQDKEVTLEY 533
Cdd:cd12314      1 NLIRLIGVPETATKEQILNAFRVPDGMPVKNLKLKNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78
OCRE super family cl23757
OCRE domain; The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which ...
 766-825 3.51e-13

OCRE domain; The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which were shown to form beta-strands. Based on the architectures of proteins containing OCRE domains, a role in RNA metabolism and/or signalling has been proposed.


The actual alignment was detected with superfamily member cd16163:

Pssm-ID: 304914 [Multi-domain]  Cd Length: 57  Bit Score: 65.06  E-value: 3.51e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  766 RGGGRNSDWSSDTNrqgqqsssDCYIYDSATGYYYDPLAGTYYDPNTqQEVYVPQDPGLP 825
Cdd:cd16163      1 EGSGPAPTYRSDPD--------SGYIYDPETGYYYDPVTGLYYDPAT-GEYVDPDTGTLP 51
YjbI COG1357
Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];
94-259 5.85e-09

Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];


:

Pssm-ID: 440968 [Multi-domain]  Cd Length: 178  Bit Score: 56.49  E-value: 5.85e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280   94 DFRGGDFSSSDFQSRDSSQLDFRGRDIhSGDFRDREGPPMDYRGGDGTSMDYRGREAPHMNYRDRDAHAVDFRGrdappS 173
Cdd:COG1357      1 DLSGADLSGADLSGADLSGADLSGANL-SGALSGANLSGANLSGANLTGANLSGADLSGADLSGANLSGADLSG-----A 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  174 DFRG---RGTYDLDFRGRDGSHADFRGRDLSDLDFRAREQSRSDFRNRDVSDLDFRDKDGTQVDFRGrgsgtTDL---DF 247
Cdd:COG1357     75 NLTGadlSGANLANLSGANLSGANLSGANLRGANLSGANLSGADLSGADLSGANLSGADLSGANLSG-----ANLsgaDL 149

                          170
                   ....*....|..
gi 2462586280  248 RDRDTPHSDFRG 259
Cdd:COG1357    150 SGADLSGANLSG 161
 
Name Accession Description Interval E-value
RRM2_RBM6 cd12563
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup ...
 654-740 6.08e-50

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409979 [Multi-domain]  Cd Length: 87  Bit Score: 170.80  E-value: 6.08e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  654 ESKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMV 733
Cdd:cd12563      1 DSKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNKTGPMGHTYGFIDLDSHAEALRLVKLLQNLDPPLYIDGRRV 80


                   ....*..
gi 2462586280  734 AVNLATG 740
Cdd:cd12563     81 YVNVATG 87
RRM1_RBM6 cd12314
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This ...
 456-533 6.52e-46

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409753 [Multi-domain]  Cd Length: 78  Bit Score: 158.89  E-value: 6.52e-46
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462586280  456 RLIRLSGVPEDATKEEILNAFRTPDGMPVKNLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIQDKEVTLEY 533
Cdd:cd12314      1 NLIRLIGVPETATKEQILNAFRVPDGMPVKNLKLKNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78
OCRE_RBM6 cd16163
OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins; RBM6, also called lung ...
 766-825 3.51e-13

OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins; RBM6, also called lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both specifically binds poly(G) RNA. RBM6 contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has an additional unique domain, the POZ (poxvirus and zinc finger) domain, which may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 293882 [Multi-domain]  Cd Length: 57  Bit Score: 65.06  E-value: 3.51e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  766 RGGGRNSDWSSDTNrqgqqsssDCYIYDSATGYYYDPLAGTYYDPNTqQEVYVPQDPGLP 825
Cdd:cd16163      1 EGSGPAPTYRSDPD--------SGYIYDPETGYYYDPVTGLYYDPAT-GEYVDPDTGTLP 51
OCRE pfam17780
OCRE domain; The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with ...
 786-818 1.45e-09

OCRE domain; The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. The structure of the domain consists of an anti-parallel arrangement of six beta strands.


Pssm-ID: 465502  Cd Length: 51  Bit Score: 54.56  E-value: 1.45e-09
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2462586280  786 SSDCYIYDSATGYYYDPLAGTYYDPNTQQEVYV 818
Cdd:pfam17780    1 DSSGYVYDEASGYYYDPTTGYYYDPNTGLYYDP 33
YjbI COG1357
Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];
94-259 5.85e-09

Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];


Pssm-ID: 440968 [Multi-domain]  Cd Length: 178  Bit Score: 56.49  E-value: 5.85e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280   94 DFRGGDFSSSDFQSRDSSQLDFRGRDIhSGDFRDREGPPMDYRGGDGTSMDYRGREAPHMNYRDRDAHAVDFRGrdappS 173
Cdd:COG1357      1 DLSGADLSGADLSGADLSGADLSGANL-SGALSGANLSGANLSGANLTGANLSGADLSGADLSGANLSGADLSG-----A 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  174 DFRG---RGTYDLDFRGRDGSHADFRGRDLSDLDFRAREQSRSDFRNRDVSDLDFRDKDGTQVDFRGrgsgtTDL---DF 247
Cdd:COG1357     75 NLTGadlSGANLANLSGANLSGANLSGANLRGANLSGANLSGADLSGADLSGANLSGADLSGANLSG-----ANLsgaDL 149

                          170
                   ....*....|..
gi 2462586280  248 RDRDTPHSDFRG 259
Cdd:COG1357    150 SGADLSGANLSG 161
RRM smart00360
RNA recognition motif;
458-531 3.39e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.97  E-value: 3.39e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462586280   458 IRLSGVPEDATKEEILNAFRtPDGmPVKNLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIQDKEVTL 531
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFS-KFG-KVESVRLvRDKETGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 458-530 8.51e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 38.75  E-value: 8.51e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462586280  458 IRLSGVPEDATKEEILNAFRtPDGmPVKNLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIQDKEVT 530
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFS-KFG-PIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGRELK 70
RRM smart00360
RNA recognition motif;
657-735 3.88e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.19  E-value: 3.88e-03
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462586280   657 TIMLKRIYRSTPPEVIVEVLEPYVRLTtaNVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNldppFSIDGKMVAV 735
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVE--SVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG----KELDGRPLKV 73
 
Name Accession Description Interval E-value
RRM2_RBM6 cd12563
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup ...
 654-740 6.08e-50

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409979 [Multi-domain]  Cd Length: 87  Bit Score: 170.80  E-value: 6.08e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  654 ESKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMV 733
Cdd:cd12563      1 DSKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNKTGPMGHTYGFIDLDSHAEALRLVKLLQNLDPPLYIDGRRV 80


                   ....*..
gi 2462586280  734 AVNLATG 740
Cdd:cd12563     81 YVNVATG 87
RRM1_RBM6 cd12314
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This ...
 456-533 6.52e-46

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409753 [Multi-domain]  Cd Length: 78  Bit Score: 158.89  E-value: 6.52e-46
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462586280  456 RLIRLSGVPEDATKEEILNAFRTPDGMPVKNLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIQDKEVTLEY 533
Cdd:cd12314      1 NLIRLIGVPETATKEQILNAFRVPDGMPVKNLKLKNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
 654-738 1.52e-28

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 109.66  E-value: 1.52e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  654 ESKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMV 733
Cdd:cd12313      1 PTNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLLPPFKIDGRVV 80


                   ....*
gi 2462586280  734 AVNLA 738
Cdd:cd12313     81 SVSYA 85
RRM2_RBM5_like cd12562
RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
 657-738 4.89e-16

RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409978 [Multi-domain]  Cd Length: 86  Bit Score: 74.21  E-value: 4.89e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  657 TIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMVAVN 736
Cdd:cd12562      4 TIILRNINPHTTVDSILGALAPYAVLSSSNVRLIKDKQTQLNRGFAFVQLSSPIEASQLLQILQSLHPPLTIDGKTINVD 83


                   ..
gi 2462586280  737 LA 738
Cdd:cd12562     84 FA 85
RRM2_RBM10 cd12754
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This ...
 657-740 3.59e-15

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410148 [Multi-domain]  Cd Length: 87  Bit Score: 71.58  E-value: 3.59e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  657 TIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMVAVN 736
Cdd:cd12754      4 TIILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTINVE 83


                   ....
gi 2462586280  737 LATG 740
Cdd:cd12754     84 FAKG 87
RRM2_RBM5 cd12755
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
 655-738 3.64e-14

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410149 [Multi-domain]  Cd Length: 86  Bit Score: 68.80  E-value: 3.64e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  655 SKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNLDPPFSIDGKMVA 734
Cdd:cd12755      2 SDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIG 81


                   ....
gi 2462586280  735 VNLA 738
Cdd:cd12755     82 VDFA 85
OCRE_RBM6 cd16163
OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins; RBM6, also called lung ...
 766-825 3.51e-13

OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins; RBM6, also called lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both specifically binds poly(G) RNA. RBM6 contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has an additional unique domain, the POZ (poxvirus and zinc finger) domain, which may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 293882 [Multi-domain]  Cd Length: 57  Bit Score: 65.06  E-value: 3.51e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  766 RGGGRNSDWSSDTNrqgqqsssDCYIYDSATGYYYDPLAGTYYDPNTqQEVYVPQDPGLP 825
Cdd:cd16163      1 EGSGPAPTYRSDPD--------SGYIYDPETGYYYDPVTGLYYDPAT-GEYVDPDTGTLP 51
RRM1_RBM5 cd12752
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
 451-533 1.28e-09

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410146 [Multi-domain]  Cd Length: 87  Bit Score: 55.72  E-value: 1.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  451 EEKPSRLIRLSGVP---EDATKEEILNAFRTPDGMPVKNLQLKeynTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIQDK 527
Cdd:cd12752      1 DEKESKTIMLRGLPiniTENDIRELIESFEGPQPADVRLMKRK---TGVSRGFAFVEFYHLQDATSWMEANQKKLVIQGK 77


                   ....*.
gi 2462586280  528 EVTLEY 533
Cdd:cd12752     78 TIAMHY 83
OCRE pfam17780
OCRE domain; The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with ...
 786-818 1.45e-09

OCRE domain; The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. The structure of the domain consists of an anti-parallel arrangement of six beta strands.


Pssm-ID: 465502  Cd Length: 51  Bit Score: 54.56  E-value: 1.45e-09
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2462586280  786 SSDCYIYDSATGYYYDPLAGTYYDPNTQQEVYV 818
Cdd:pfam17780    1 DSSGYVYDEASGYYYDPTTGYYYDPNTGLYYDP 33
RRM1_RBM10 cd12753
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This ...
 455-533 3.88e-09

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410147 [Multi-domain]  Cd Length: 84  Bit Score: 54.56  E-value: 3.88e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462586280  455 SRLIRLSGVPEDATKEEILNAFRTPDGMPVKNLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIQDKEVTLEY 533
Cdd:cd12753      1 SNIIMLRMLPQSATENDIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVSMHY 79
OCRE cd16074
OCRE domain; The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which ...
 767-825 5.06e-09

OCRE domain; The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which were shown to form beta-strands. Based on the architectures of proteins containing OCRE domains, a role in RNA metabolism and/or signalling has been proposed.


Pssm-ID: 293880  Cd Length: 54  Bit Score: 53.06  E-value: 5.06e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462586280  767 GGGRNSDWSSDTNrqgqqsssDCYIYDSATGYYYDPLAGTYYDPNTQQevYVPQDPGLP 825
Cdd:cd16074      1 GSPDPSGFVFDPN--------SGYYYDPSTGLYYDPNTGYYYDPTSGT--YYIWDDELG 49
YjbI COG1357
Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];
94-259 5.85e-09

Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];


Pssm-ID: 440968 [Multi-domain]  Cd Length: 178  Bit Score: 56.49  E-value: 5.85e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280   94 DFRGGDFSSSDFQSRDSSQLDFRGRDIhSGDFRDREGPPMDYRGGDGTSMDYRGREAPHMNYRDRDAHAVDFRGrdappS 173
Cdd:COG1357      1 DLSGADLSGADLSGADLSGADLSGANL-SGALSGANLSGANLSGANLTGANLSGADLSGADLSGANLSGADLSG-----A 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  174 DFRG---RGTYDLDFRGRDGSHADFRGRDLSDLDFRAREQSRSDFRNRDVSDLDFRDKDGTQVDFRGrgsgtTDL---DF 247
Cdd:COG1357     75 NLTGadlSGANLANLSGANLSGANLSGANLRGANLSGANLSGADLSGADLSGANLSGADLSGANLSG-----ANLsgaDL 149

                          170
                   ....*....|..
gi 2462586280  248 RDRDTPHSDFRG 259
Cdd:COG1357    150 SGADLSGANLSG 161
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
 454-533 2.55e-08

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 51.98  E-value: 2.55e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  454 PSRLIRLSGVPEDATKEEILNAFRTPDGMPVKNLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTLMIQDKEVTLEY 533
Cdd:cd12561      1 PNNTIMLRGLPLSVTEEDIRNALVSHGVQPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMEANQGKLQLQGYKITLHY 80
OCRE_RBM5 cd16168
OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called ...
 790-813 5.96e-08

OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 293887  Cd Length: 56  Bit Score: 50.10  E-value: 5.96e-08
                           10        20
                   ....*....|....*....|....
gi 2462586280  790 YIYDSATGYYYDPLAGTYYDPNTQ 813
Cdd:cd16168      8 YQYDESSGYYYDPITGLYYDPNSQ 31
OCRE_RBM5_like cd16162
OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known ...
 790-813 4.50e-07

OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing, and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 293881  Cd Length: 56  Bit Score: 47.70  E-value: 4.50e-07
                           10        20
                   ....*....|....*....|....
gi 2462586280  790 YIYDSATGYYYDPLAGTYYDPNTQ 813
Cdd:cd16162      8 YQYDETSGYYYDPTTGLYYDPNSQ 31
OCRE_RBM10 cd16167
OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G ...
 790-813 9.59e-07

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 293886  Cd Length: 64  Bit Score: 46.98  E-value: 9.59e-07
                           10        20
                   ....*....|....*....|....
gi 2462586280  790 YIYDSATGYYYDPLAGTYYDPNTQ 813
Cdd:cd16167      9 YQYDETSGYYYDPQTGLYYDPNSQ 32
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
 454-533 1.57e-06

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 46.88  E-value: 1.57e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280  454 PSRLIRLSGVPEDATKEEILNAFRTPDGMPVKNLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGT---LMIQDKEV 529
Cdd:cd12313      1 PTNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLiRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLlppFKIDGRVV 80


                   ....
gi 2462586280  530 TLEY 533
Cdd:cd12313     81 SVSY 84
OCRE_RBM5_like cd16162
OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known ...
 790-817 1.68e-06

OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing, and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 293881  Cd Length: 56  Bit Score: 46.15  E-value: 1.68e-06
                           10        20
                   ....*....|....*....|....*...
gi 2462586280  790 YIYDSATGYYYDPLAGTYYDPNTQQEVY 817
Cdd:cd16162     16 YYYDPTTGLYYDPNSQYFYNSQTQQYLY 43
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 458-532 4.00e-06

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 45.35  E-value: 4.00e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462586280  458 IRLSGVPEDATKEEILNAFRtPDGmPVKNLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIQDKEVTLE 532
Cdd:cd00590      1 LFVGNLPPDTTEEDLRELFS-KFG-EVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGT-ELGGRPLKVS 72
OCRE_SUA_like cd16166
OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding ...
 790-813 1.54e-05

OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding protein located in the nucleus and expressed in all plant tissues. It functions as a splicing factor that influences seed maturation by controlling alternative splicing of ABI3. The suppression of the cryptic ABI3 intron indicates a role of SUA in mRNA processing. SUA also interacts with the prespliceosomal component U2AF65, the larger subunit of the conserved pre-mRNA splicing factor U2AF. SUA contains two RNA recognition motifs surrounding a zinc finger domain, an OCtamer REpeat (OCRE) domain, and a Gly-rich domain close to the C-terminus.


Pssm-ID: 293885  Cd Length: 54  Bit Score: 43.05  E-value: 1.54e-05
                           10        20
                   ....*....|....*....|....
gi 2462586280  790 YIYDSATGYYYDPLAGTYYDPNTQ 813
Cdd:cd16166      8 FVYDPASGYYYDASSGYYYDANTG 31
RRM smart00360
RNA recognition motif;
458-531 3.39e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.97  E-value: 3.39e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462586280   458 IRLSGVPEDATKEEILNAFRtPDGmPVKNLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIQDKEVTL 531
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFS-KFG-KVESVRLvRDKETGKSKGFAFVEFESEEDAEKALEALNGK-ELDGRPLKV 73
OCRE_VG5Q cd16164
OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic ...
 790-813 3.53e-05

OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic factor with G patch and FHA domains 1 (AGGF1), or G patch domain-containing protein 7, or vasculogenesis gene on 5q protein, functions as a potent angiogenic factor in promoting angiogenesis through interacting with TWEAK (also known as TNFSF12), which is a member of the tumor necrosis factor (TNF) superfamily that induces angiogenesis in vivo. VG5Q can bind to the surface of endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. The chromosomal translocation t(5;11) and the E133K variant in VG5Q are associated with Klippel-Trenaunay syndrome (KTS), a disorder characterized by diverse effects in the vascular system. In addition to a forkhead-associated (FHA) domain and a G-patch motif, VG5Q contains an N-terminal OCtamer REpeat (OCRE) domain that is characterized by a 5-fold, imperfectly repeated octameric sequence.


Pssm-ID: 293883  Cd Length: 54  Bit Score: 42.27  E-value: 3.53e-05
                           10        20
                   ....*....|....*....|....
gi 2462586280  790 YIYDSATGYYYDPLAGTYYDPNTQ 813
Cdd:cd16164      8 FVYDEATGMYYDPSTGYYYDSETQ 31
YjbI COG1357
Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];
94-235 3.85e-05

Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown];


Pssm-ID: 440968 [Multi-domain]  Cd Length: 178  Bit Score: 45.32  E-value: 3.85e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462586280   94 DFRGGDFSSSDFQSRDSSQLDFRGRDIHSGDFRDregppMDYRGGDGTSMDYRGreAPHMNYRDRDAHAVDFRGRDAPPS 173
Cdd:COG1357     35 NLSGANLSGANLTGANLSGADLSGADLSGANLSG-----ADLSGANLTGADLSG--ANLANLSGANLSGANLSGANLRGA 107

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462586280  174 DFRG---RGTydlDFRGRDGSHADFRGRDLSDLDFRAREQSRSDFRNRDVSDLDFRDKDGTQVDF 235
Cdd:COG1357    108 NLSGanlSGA---DLSGADLSGANLSGADLSGANLSGANLSGADLSGADLSGANLSGANLSGANL 169
OCRE_RBM5 cd16168
OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called ...
 783-817 4.36e-05

OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 293887  Cd Length: 56  Bit Score: 42.02  E-value: 4.36e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2462586280  783 QQSSSDCYIYDSATGYYYDPLAGTYYDPNTQQEVY 817
Cdd:cd16168      9 QYDESSGYYYDPITGLYYDPNSQYYYNSLTQQYLY 43
OCRE_ZOP1_plant cd16165
OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar ...
 768-825 1.26e-04

OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar proteins found in plant; ZOP1 is a novel plant-specific nucleic acid-binding protein required for both RNA-directed DNA methylation (RdDM) and pre-mRNA splicing. It promotes RNA polymerase IV (Pol IV)-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. As a pre-mRNA splicing factor, ZOP1 associates with several typical splicing proteins as well as with RNA polymerase II (RNAP II and Pol II). It also shows both RdDM-dependent and -independent roles in transcriptional silencing. ZOP1 contains an N-terminal C2H2-type ZnF domain and an OCtamer REpeat (OCRE) domain that is usually related to RNA processing.


Pssm-ID: 293884  Cd Length: 55  Bit Score: 40.84  E-value: 1.26e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462586280  768 GGRNSDWSSDtnrqgqqSSSDcYIYDSATGYYYDPLAGTYYDPNTQQEVYVPQDPGLP 825
Cdd:cd16165      2 ADGAGDWVLD-------SKSG-YYYNAATRYYYDPKTGMYYSDETGKWTTQPPEHAEA 51
OCRE_VG5Q cd16164
OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic ...
 792-812 1.48e-04

OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic factor with G patch and FHA domains 1 (AGGF1), or G patch domain-containing protein 7, or vasculogenesis gene on 5q protein, functions as a potent angiogenic factor in promoting angiogenesis through interacting with TWEAK (also known as TNFSF12), which is a member of the tumor necrosis factor (TNF) superfamily that induces angiogenesis in vivo. VG5Q can bind to the surface of endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. The chromosomal translocation t(5;11) and the E133K variant in VG5Q are associated with Klippel-Trenaunay syndrome (KTS), a disorder characterized by diverse effects in the vascular system. In addition to a forkhead-associated (FHA) domain and a G-patch motif, VG5Q contains an N-terminal OCtamer REpeat (OCRE) domain that is characterized by a 5-fold, imperfectly repeated octameric sequence.


Pssm-ID: 293883  Cd Length: 54  Bit Score: 40.34  E-value: 1.48e-04
                           10        20
                   ....*....|....*....|.
gi 2462586280  792 YDSATGYYYDPLAGTYYDPNT 812
Cdd:cd16164     18 YDPSTGYYYDSETQLYYDPNT 38
OCRE_SUA_like cd16166
OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding ...
 790-814 2.56e-04

OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding protein located in the nucleus and expressed in all plant tissues. It functions as a splicing factor that influences seed maturation by controlling alternative splicing of ABI3. The suppression of the cryptic ABI3 intron indicates a role of SUA in mRNA processing. SUA also interacts with the prespliceosomal component U2AF65, the larger subunit of the conserved pre-mRNA splicing factor U2AF. SUA contains two RNA recognition motifs surrounding a zinc finger domain, an OCtamer REpeat (OCRE) domain, and a Gly-rich domain close to the C-terminus.


Pssm-ID: 293885  Cd Length: 54  Bit Score: 39.97  E-value: 2.56e-04
                           10        20
                   ....*....|....*....|....*
gi 2462586280  790 YIYDSATGYYYDPLAGTYYDPNTQQ 814
Cdd:cd16166     16 YYYDASSGYYYDANTGLYYDAASGR 40
OCRE_VG5Q cd16164
OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic ...
 768-818 5.94e-04

OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic factor with G patch and FHA domains 1 (AGGF1), or G patch domain-containing protein 7, or vasculogenesis gene on 5q protein, functions as a potent angiogenic factor in promoting angiogenesis through interacting with TWEAK (also known as TNFSF12), which is a member of the tumor necrosis factor (TNF) superfamily that induces angiogenesis in vivo. VG5Q can bind to the surface of endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. The chromosomal translocation t(5;11) and the E133K variant in VG5Q are associated with Klippel-Trenaunay syndrome (KTS), a disorder characterized by diverse effects in the vascular system. In addition to a forkhead-associated (FHA) domain and a G-patch motif, VG5Q contains an N-terminal OCtamer REpeat (OCRE) domain that is characterized by a 5-fold, imperfectly repeated octameric sequence.


Pssm-ID: 293883  Cd Length: 54  Bit Score: 38.80  E-value: 5.94e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2462586280  768 GGRNSDWSSDTNRQGQQSSSDCYIYDSATGYYYDPLAGTYY--DPNTQQEVYV 818
Cdd:cd16164      2 AVSQSGFVYDEATGMYYDPSTGYYYDSETQLYYDPNTGTYYyyDEESGSYQFH 54
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 458-530 8.51e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 38.75  E-value: 8.51e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462586280  458 IRLSGVPEDATKEEILNAFRtPDGmPVKNLQLKEYNTGYDYGYVCVEFSLLEDAIGCMEANQGTlMIQDKEVT 530
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFS-KFG-PIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGRELK 70
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
 463-533 9.78e-04

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 38.92  E-value: 9.78e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462586280  463 VPEDATKEEILNAFRTPDgmPVKNLQL-KEYNTGYDYGYVCVEFSLLEDAIGCMEANQGtLMIQDKEVTLEY 533
Cdd:cd12649      8 LPQDLTDREFRALFRAIG--PVNTCKIvRDKKTGYSYGFGFVDFTSEEDAQRAIKTLNG-LQLQNKRLKVAY 76
OCRE_RBM10 cd16167
OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G ...
 783-817 1.22e-03

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 293886  Cd Length: 64  Bit Score: 38.12  E-value: 1.22e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2462586280  783 QQSSSDCYIYDSATGYYYDPLAGTYYDPNTQQEVY 817
Cdd:cd16167     10 QYDETSGYYYDPQTGLYYDPNSQYYYNAQTQQYLY 44
RRM smart00360
RNA recognition motif;
657-735 3.88e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.19  E-value: 3.88e-03
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462586280   657 TIMLKRIYRSTPPEVIVEVLEPYVRLTtaNVRIIKNRTGPMGHTYGFIDLDSHAEALRVVKILQNldppFSIDGKMVAV 735
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVE--SVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG----KELDGRPLKV 73
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
 457-521 9.70e-03

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 36.44  E-value: 9.70e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462586280  457 LIRLSGVPEDATKEEILNAFRTpDGmPVKNLQLK-EYNTGYDYGYVCVEFSLLEDAIGCMEANQGT 521
Cdd:cd12324      8 IIFVTGVHEEAQEEDIHDKFAE-FG-EIKNLHLNlDRRTGFVKGYALVEYETKKEAQAAIEGLNGK 71
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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