RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17538402  93 STLIIKNLATTVTQEDLEELFEQ-YEPELVQLHYGPTGESNGCADLIVPH-AQVAIIQKALEGVLLDGEPIEV 163
Cdd:cd12418   1 TRVRVSNLHPDVTEEDLRELFGRvGPVKSVKINYDRSGRSTGTAYVVFERpEDAEKAIKQFDGVLLDGQPMKV 73

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17538402  93 STLIIKNLATTVTQEDLEELFEQ-YEPELVQLHYGPTGESNGCADLIVPH-AQVAIIQKALEGVLLDGEPIEV 163
Cdd:cd12418   1 TRVRVSNLHPDVTEEDLRELFGRvGPVKSVKINYDRSGRSTGTAYVVFERpEDAEKAIKQFDGVLLDGQPMKV 73

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17538402     94 TLIIKNLATTVTQEDLEELFEQYEP-ELVQLHYGP-TGESNGCAdlIV-----PHAQVAIiqKALEGVLLDGEPIEV 163
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKvESVRLVRDKeTGKSKGFA--FVefeseEDAEKAL--EALNGKELDGRPLKV 73

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17538402    95 LIIKNLATTVTQEDLEELFEQYEPELVQ----------LHYgptgESNGCAdlivPHAqvaiiQKALEGVLLDGEPIEVL 164
Cdd:TIGR01648 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVErvkkirdyafVHF----EDREDA----VKA-----MDELNGKELEGSEIEVT 302

                          90       100
                  ....*....|....*....|..
gi 17538402   165 EANPP--KQVSVFDRIKKVSRG 184
Cdd:TIGR01648 303 LAKPVdkKSYVRYTRGTGGRGK 324

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17538402  93 STLIIKNLATTVTQEDLEELFEQ-YEPELVQLHYGPTGESNGCADLIVPH-AQVAIIQKALEGVLLDGEPIEV 163
Cdd:cd12418   1 TRVRVSNLHPDVTEEDLRELFGRvGPVKSVKINYDRSGRSTGTAYVVFERpEDAEKAIKQFDGVLLDGQPMKV 73

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17538402    95 LIIKNLATTVTQEDLEELFEQYEPEL-VQLHYGPTGESNGCAdlIVPHAQVAIIQKALE---GVLLDGEPIE 162
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKsIRLVRDETGRSKGFA--FVEFEDEEDAEKAIEalnGKELGGRELK 70

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17538402  94 TLIIKNLATTVTQEDLEELFEQY----EPELVQLHYgpTGESNGCADLIVP---HAQVAIiqKALEGVLLDGEPIEVLEA 166
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSEYgevtSVKLITDRE--TGRSRGFGFVEMPddeEAQAAI--EALNGAELMGRTLKVNEA 78

                ....*
gi 17538402 167 NPPKQ 171
Cdd:COG0724  79 RPREE 83

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                        10        20        30
                ....*....|....*....|....*....|.
gi 17538402  95 LIIKNLATTVTQEDLEELFEQYEPeLVQLHY 125
Cdd:cd12567   5 LFVRNLPYTCTEEDLEKLFSKYGP-LSEVHF 34

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17538402  95 LIIKNLATTVTQEDLEELFEQYEPEL-VQLHYGPTGESNGCADL---IVPHAQVAIiqKALEGVLLDGEPIEV 163
Cdd:cd12414   2 LIVRNLPFKCTEDDLKKLFSKFGKVLeVTIPKKPDGKLRGFAFVqftNVADAAKAI--KGMNGKKIKGRPVAV 72

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17538402  95 LIIKNLATTVTQEDLEELFEQYePELVQLHY---GPTGESNGCAD---LIVPHAQVAIiqKALEGVLLDGEPIEVL 164
Cdd:cd12316   2 LFVRNLPFTATEDELRELFEAF-GKISEVHIpldKQTKRSKGFAFvlfVIPEDAVKAY--QELDGSIFQGRLLHVL 74

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17538402  93 STLIIKNLATTVTQEDLEELFEQY------EPELVQLHYGPTGESNGCADLIVPHAQVAiiQKALE---GVLLDGEPIEV 163
Cdd:cd12239   2 NRLYVKNLSKRVSEKDLKYIFGRFvdssseEKNMFDIRLMTEGRMKGQAFITFPSEELA--EKALNltnGYVLHGKPMVV 79

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17538402  94 TLIIKNLATTVTQEDLEELFEQY-EPELVQLHYGP-TGESNGCADLIVPHAQVAiiQKALE---------GVLLDGEPIE 162
Cdd:cd12415   2 TVFIRNLSFDTTEEDLKEFFSKFgEVKYARIVLDKdTGHSKGTAFVQFKTKESA--DKCIEaandesedgGLVLDGRKLI 79

                ....
gi 17538402 163 VLEA 166
Cdd:cd12415  80 VSLA 83