NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|564341547|ref|XP_006234487|]
View 

pre-mRNA-splicing factor CWC22 homolog isoform X3 [Rattus norvegicus]

Protein Classification

MIF4G domain-containing protein; EIF4G1 family eukaryotic translation initiation factor( domain architecture ID 13919211)

MIF4G (middle domain of eukaryotic initiation factor 4G) domain-containing protein may contain multiple alpha-helical repeats; similar to Oryza sativa eukaryotic translation initiation factor 4 gamma (EIF4G), which plays a key functional role in the initiation of cap-dependent translation by acting as an adapter to nucleate the assembly of eIF4F complex| EIF4G1 family eukaryotic translation initiation factor similar to eukaryotic translation initiation factor 4 gamma 1 (EIF4G1), a component of the protein complex eIF4F, which is involved in the recognition of the mRNA cap, ATP-dependent unwinding of 5'-terminal secondary structure and recruitment of mRNA to the ribosome

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 164-345 6.01e-23

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


:

Pssm-ID: 214713  Cd Length: 200  Bit Score: 97.43  E-value: 6.01e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547   164 KSINGLINKVNISNISIIIQELLQENIVRG--RGLLSRSVLQAQSASPIFTHVYAALVAIINSKFPQIGELILKRLILNF 241
Cdd:smart00543   2 KKVKGLINKLSPSNFESIIKELLKLNNSDKnlRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEF 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547   242 RKG---YRRNDKQLCLTASKFVAHLINQNVAHEVLCLEMLTLLLERPT-------DDSVEVAIGFLKECGLKLT-QVSPR 310
Cdd:smart00543  82 EKGlesEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTkldpprsDFSVECLLSLLPTCGKDLErEKSPK 161

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 564341547   311 GINAIFERLRNILHES---EIDKRVQYMIEVMFAVRKD 345
Cdd:smart00543 162 LLDEILERLQDYLLKKdktELSSRLRFMLELLIELRKN 199
MA3 super family cl02653
MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain ...
 456-562 5.32e-20

MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains.


The actual alignment was detected with superfamily member pfam02847:

Pssm-ID: 413424  Cd Length: 113  Bit Score: 86.18  E-value: 5.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  456 FRRTIYLAIQSSL---DFEECAHKLLKMEfAESQTKELCNMILDCCAQQ-RTYEKFFGLLAGRFCMLKKEYMESFESIFK 531
Cdd:pfam02847   1 LKRKIFLILEEYLssgDYDEAARCLLKLG-LPSQHHEVVKVLIECALEEsKTYREFYGLLLERLCEFNLISTKQFEKGFW 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 564341547  532 EQYDTIHRLET---NKLRNVAKMFAHLLYTDSLP 562
Cdd:pfam02847  80 RVLEDLEDLELdipNAWRNLAEFVARLISDDGLP 113
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 824-903 1.51e-06

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


The actual alignment was detected with superfamily member TIGR01642:

Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.82  E-value: 1.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  824 DSFSENEKQRARNQDSDNVRRKDGSKSRERSRKHSG--HKGDDDDRYQNGAERRWEKPSRYAEHSRESKRSQDRRREKSP 901
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSreRSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85


                  ..
gi 564341547  902 TK 903
Cdd:TIGR01642  86 RS 87
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 728-897 2.91e-05

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 47.98  E-value: 2.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547 728 EEVDKLARSHQARDRRREGGREDQRHQEGRTERARSERHRAQHSRDADWRDPPAKHMEDRSHENSyNRVGNGREQGSHRE 807
Cdd:PRK12678 121 APEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEA-ERGERGRREERGRD 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547 808 PEDRhgepRKKRRERRDSFSENEKQRARNQDSDNVRRKDGSKSRERSRKHSGHKGDDDDRYQNGAERRwekpsryaehsr 887
Cdd:PRK12678 200 GDDR----DRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRG------------ 263

                        170
                 ....*....|
gi 564341547 888 esKRSQDRRR 897
Cdd:PRK12678 264 --RRFRDRDR 271
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 9-106 3.45e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


The actual alignment was detected with superfamily member TIGR01642:

Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 41.03  E-value: 3.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547    9 KSSGHDRRESHNSyHRRSSSPEDRYTEQDRSPRDRDYSDYSRSDYERSRRGYSYDDSMESRSR-------DREKRRERER 81
Cdd:TIGR01642  11 KSRGRDRDRSSER-PRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRrsrdrprRRSRSVRSIE 89

                          90       100
                  ....*....|....*....|....*
gi 564341547   82 DADHRKRSRkSPSPERRSPDRGVSQ 106
Cdd:TIGR01642  90 QHRRRLRDR-SPSNQWRKDDKKRSL 113
 
Name Accession Description Interval E-value
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 164-345 6.01e-23

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


Pssm-ID: 214713  Cd Length: 200  Bit Score: 97.43  E-value: 6.01e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547   164 KSINGLINKVNISNISIIIQELLQENIVRG--RGLLSRSVLQAQSASPIFTHVYAALVAIINSKFPQIGELILKRLILNF 241
Cdd:smart00543   2 KKVKGLINKLSPSNFESIIKELLKLNNSDKnlRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEF 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547   242 RKG---YRRNDKQLCLTASKFVAHLINQNVAHEVLCLEMLTLLLERPT-------DDSVEVAIGFLKECGLKLT-QVSPR 310
Cdd:smart00543  82 EKGlesEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTkldpprsDFSVECLLSLLPTCGKDLErEKSPK 161

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 564341547   311 GINAIFERLRNILHES---EIDKRVQYMIEVMFAVRKD 345
Cdd:smart00543 162 LLDEILERLQDYLLKKdktELSSRLRFMLELLIELRKN 199
MA3 pfam02847
MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain ...
 456-562 5.32e-20

MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains.


Pssm-ID: 397128  Cd Length: 113  Bit Score: 86.18  E-value: 5.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  456 FRRTIYLAIQSSL---DFEECAHKLLKMEfAESQTKELCNMILDCCAQQ-RTYEKFFGLLAGRFCMLKKEYMESFESIFK 531
Cdd:pfam02847   1 LKRKIFLILEEYLssgDYDEAARCLLKLG-LPSQHHEVVKVLIECALEEsKTYREFYGLLLERLCEFNLISTKQFEKGFW 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 564341547  532 EQYDTIHRLET---NKLRNVAKMFAHLLYTDSLP 562
Cdd:pfam02847  80 RVLEDLEDLELdipNAWRNLAEFVARLISDDGLP 113
MA3 smart00544
Domain in DAP-5, eIF4G, MA-3 and other proteins; Highly alpha-helical. May contain repeats and ...
 456-562 2.18e-18

Domain in DAP-5, eIF4G, MA-3 and other proteins; Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press


Pssm-ID: 214714  Cd Length: 113  Bit Score: 81.52  E-value: 2.18e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547   456 FRRTIYLAIQSSL---DFEECAHKLLKMEFAEsQTKELCNMILDCCAQQ-RTYEKFFGLLAGRFCMLKKEYMESFESIFK 531
Cdd:smart00544   1 LKKKIFLIIEEYLssgDTDEAVHCLLELKLPE-QHHEVVKVLLTCALEEkRTYREMYSVLLSRLCQANVISTKQFEKGFW 79

                           90       100       110
                   ....*....|....*....|....*....|....
gi 564341547   532 EQYDTIHRLET---NKLRNVAKMFAHLLYTDSLP 562
Cdd:smart00544  80 RLLEDIEDLELdipNAWRNLAEFVARLISDGILP 113
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 824-903 1.51e-06

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.82  E-value: 1.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  824 DSFSENEKQRARNQDSDNVRRKDGSKSRERSRKHSG--HKGDDDDRYQNGAERRWEKPSRYAEHSRESKRSQDRRREKSP 901
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSreRSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85


                  ..
gi 564341547  902 TK 903
Cdd:TIGR01642  86 RS 87
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 728-897 2.91e-05

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 47.98  E-value: 2.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547 728 EEVDKLARSHQARDRRREGGREDQRHQEGRTERARSERHRAQHSRDADWRDPPAKHMEDRSHENSyNRVGNGREQGSHRE 807
Cdd:PRK12678 121 APEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEA-ERGERGRREERGRD 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547 808 PEDRhgepRKKRRERRDSFSENEKQRARNQDSDNVRRKDGSKSRERSRKHSGHKGDDDDRYQNGAERRwekpsryaehsr 887
Cdd:PRK12678 200 GDDR----DRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRG------------ 263

                        170
                 ....*....|
gi 564341547 888 esKRSQDRRR 897
Cdd:PRK12678 264 --RRFRDRDR 271
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 164-345 2.91e-04

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


Pssm-ID: 397130  Cd Length: 203  Bit Score: 43.12  E-value: 2.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  164 KSINGLINKVNISNISIIIQELLQENI--VRGRGLLSRSVLQAQSASPIFTHVYAALVAIINSKFPQ-IGELILKRLILN 240
Cdd:pfam02854   2 KKVKGILNKLSPENFEKLIKELLKLIMsdPELLKYLIELIFEKAVEEPNFIPAYARLCSGLNLRNPTdFGIHLLNRLQEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  241 FRKGY--RRNDKQLCLTASKFVA--------HLINQNVAHEVLCL--EMLTLLLERPTDDSVEVAIGFLKECGLKL-TQV 307
Cdd:pfam02854  82 FEKRFelEENEQGNRRRRLGLVRflgelykfGLLTEKILFECLKEllSSLTKEDLKRDLFNLECLLTLLTTIGKLLeNEK 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 564341547  308 SPRGINAIFERLRNIL---HESEIDKRVQYMIEVMFAVRKD 345
Cdd:pfam02854 162 LPKLMDQFLDEIQKYVlskDDPKLSSRLRFMLQDLIELRKN 202
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 9-106 3.45e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 41.03  E-value: 3.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547    9 KSSGHDRRESHNSyHRRSSSPEDRYTEQDRSPRDRDYSDYSRSDYERSRRGYSYDDSMESRSR-------DREKRRERER 81
Cdd:TIGR01642  11 KSRGRDRDRSSER-PRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRrsrdrprRRSRSVRSIE 89

                          90       100
                  ....*....|....*....|....*
gi 564341547   82 DADHRKRSRkSPSPERRSPDRGVSQ 106
Cdd:TIGR01642  90 QHRRRLRDR-SPSNQWRKDDKKRSL 113
 
Name Accession Description Interval E-value
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 164-345 6.01e-23

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


Pssm-ID: 214713  Cd Length: 200  Bit Score: 97.43  E-value: 6.01e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547   164 KSINGLINKVNISNISIIIQELLQENIVRG--RGLLSRSVLQAQSASPIFTHVYAALVAIINSKFPQIGELILKRLILNF 241
Cdd:smart00543   2 KKVKGLINKLSPSNFESIIKELLKLNNSDKnlRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEF 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547   242 RKG---YRRNDKQLCLTASKFVAHLINQNVAHEVLCLEMLTLLLERPT-------DDSVEVAIGFLKECGLKLT-QVSPR 310
Cdd:smart00543  82 EKGlesEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTkldpprsDFSVECLLSLLPTCGKDLErEKSPK 161

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 564341547   311 GINAIFERLRNILHES---EIDKRVQYMIEVMFAVRKD 345
Cdd:smart00543 162 LLDEILERLQDYLLKKdktELSSRLRFMLELLIELRKN 199
MA3 pfam02847
MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain ...
 456-562 5.32e-20

MA3 domain; Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains.


Pssm-ID: 397128  Cd Length: 113  Bit Score: 86.18  E-value: 5.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  456 FRRTIYLAIQSSL---DFEECAHKLLKMEfAESQTKELCNMILDCCAQQ-RTYEKFFGLLAGRFCMLKKEYMESFESIFK 531
Cdd:pfam02847   1 LKRKIFLILEEYLssgDYDEAARCLLKLG-LPSQHHEVVKVLIECALEEsKTYREFYGLLLERLCEFNLISTKQFEKGFW 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 564341547  532 EQYDTIHRLET---NKLRNVAKMFAHLLYTDSLP 562
Cdd:pfam02847  80 RVLEDLEDLELdipNAWRNLAEFVARLISDDGLP 113
MA3 smart00544
Domain in DAP-5, eIF4G, MA-3 and other proteins; Highly alpha-helical. May contain repeats and ...
 456-562 2.18e-18

Domain in DAP-5, eIF4G, MA-3 and other proteins; Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press


Pssm-ID: 214714  Cd Length: 113  Bit Score: 81.52  E-value: 2.18e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547   456 FRRTIYLAIQSSL---DFEECAHKLLKMEFAEsQTKELCNMILDCCAQQ-RTYEKFFGLLAGRFCMLKKEYMESFESIFK 531
Cdd:smart00544   1 LKKKIFLIIEEYLssgDTDEAVHCLLELKLPE-QHHEVVKVLLTCALEEkRTYREMYSVLLSRLCQANVISTKQFEKGFW 79

                           90       100       110
                   ....*....|....*....|....*....|....
gi 564341547   532 EQYDTIHRLET---NKLRNVAKMFAHLLYTDSLP 562
Cdd:smart00544  80 RLLEDIEDLELdipNAWRNLAEFVARLISDGILP 113
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 824-903 1.51e-06

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.82  E-value: 1.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  824 DSFSENEKQRARNQDSDNVRRKDGSKSRERSRKHSG--HKGDDDDRYQNGAERRWEKPSRYAEHSRESKRSQDRRREKSP 901
Cdd:TIGR01642   6 DREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSreRSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85


                  ..
gi 564341547  902 TK 903
Cdd:TIGR01642  86 RS 87
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 728-897 2.91e-05

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 47.98  E-value: 2.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547 728 EEVDKLARSHQARDRRREGGREDQRHQEGRTERARSERHRAQHSRDADWRDPPAKHMEDRSHENSyNRVGNGREQGSHRE 807
Cdd:PRK12678 121 APEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEA-ERGERGRREERGRD 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547 808 PEDRhgepRKKRRERRDSFSENEKQRARNQDSDNVRRKDGSKSRERSRKHSGHKGDDDDRYQNGAERRwekpsryaehsr 887
Cdd:PRK12678 200 GDDR----DRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRG------------ 263

                        170
                 ....*....|
gi 564341547 888 esKRSQDRRR 897
Cdd:PRK12678 264 --RRFRDRDR 271
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 824-899 1.74e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 45.30  E-value: 1.74e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564341547  824 DSFSENEKQRARNQDSDNVRRKdgSKSRERSRKHSGHKGDDDDRYQNGAERRWEKPSRYAEHSRESKRSQDRRREK 899
Cdd:TIGR01622  12 DSSSAGDRDRRRDKGRERSRDR--SRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPREKRRRRGDSYRR 85
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 715-867 2.59e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 44.89  E-value: 2.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547 715 KGSRKKRQGKARGEEVDKLARSHQARDRRREGGREDQRHQEGRTERARSERHRAQHSRDADWRDPPAKHMEDRSHENSYN 794
Cdd:PRK12678 140 GAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERG 219

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564341547 795 RVGNGREQGSHREPEDRHGEprkkrrerrDSFSENEKQRARNQDSDNVRRKDGSKSRERSRKHSGHKGDDDDR 867
Cdd:PRK12678 220 RRDGGDRRGRRRRRDRRDAR---------GDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNER 283
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 164-345 2.91e-04

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


Pssm-ID: 397130  Cd Length: 203  Bit Score: 43.12  E-value: 2.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  164 KSINGLINKVNISNISIIIQELLQENI--VRGRGLLSRSVLQAQSASPIFTHVYAALVAIINSKFPQ-IGELILKRLILN 240
Cdd:pfam02854   2 KKVKGILNKLSPENFEKLIKELLKLIMsdPELLKYLIELIFEKAVEEPNFIPAYARLCSGLNLRNPTdFGIHLLNRLQEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  241 FRKGY--RRNDKQLCLTASKFVA--------HLINQNVAHEVLCL--EMLTLLLERPTDDSVEVAIGFLKECGLKL-TQV 307
Cdd:pfam02854  82 FEKRFelEENEQGNRRRRLGLVRflgelykfGLLTEKILFECLKEllSSLTKEDLKRDLFNLECLLTLLTTIGKLLeNEK 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 564341547  308 SPRGINAIFERLRNIL---HESEIDKRVQYMIEVMFAVRKD 345
Cdd:pfam02854 162 LPKLMDQFLDEIQKYVlskDDPKLSSRLRFMLQDLIELRKN 202
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 785-905 1.59e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 42.19  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547  785 EDRSHENSYNRVGNGREQGSHREPEDRhgeprkkrrerrdsfsenEKQRARNQDSDNVRRKDGSKSRERSRKHSGHKGDD 864
Cdd:TIGR01642   5 PDREREKSRGRDRDRSSERPRRRSRDR------------------SRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSL 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 564341547  865 DDRYQNGA---ERRWEKPSRYAEHSRESKRSQDRRREKSPTKHK 905
Cdd:TIGR01642  67 RYSSVRRSrdrPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKK 110
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 9-106 3.45e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 41.03  E-value: 3.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341547    9 KSSGHDRRESHNSyHRRSSSPEDRYTEQDRSPRDRDYSDYSRSDYERSRRGYSYDDSMESRSR-------DREKRRERER 81
Cdd:TIGR01642  11 KSRGRDRDRSSER-PRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRrsrdrprRRSRSVRSIE 89

                          90       100
                  ....*....|....*....|....*
gi 564341547   82 DADHRKRSRkSPSPERRSPDRGVSQ 106
Cdd:TIGR01642  90 QHRRRLRDR-SPSNQWRKDDKKRSL 113
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH