RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWR 247
Cdd:cd12257     1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAYRSPEAVFNNRFIKVFWH 72

Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organizms from protists to humans. They are centred by precisely organized, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1078654864 255 ENEVAEQQRLQEERQAAFEEKEQRRKEHLEKmtgiLAQKKQLLE 298
Cdd:pfam06098 170 NAELAEVQRLEEQERRLREEKERRIAQQREA----LKKEKETAE 209

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWR 247
Cdd:cd12257     1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAYRSPEAVFNNRFIKVFWH 72

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1078654864  178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV---NFAGKL---AEIEFSTTAEAKNAYKS-PETIFDNRFVKV 244
Cdd:smart00360   1 TLFVGNLPPD-TTEEELRELFSKFGKVESVRLvrdKETGKSkgfAFVEFESEEDAEKALEAlNGKELDGRPLKV 73

Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organizms from protists to humans. They are centred by precisely organized, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1078654864 255 ENEVAEQQRLQEERQAAFEEKEQRRKEHLEKmtgiLAQKKQLLE 298
Cdd:pfam06098 170 NAELAEVQRLEEQERRLREEKERRIAQQREA----LKKEKETAE 209

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWR 247
Cdd:cd12257     1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAYRSPEAVFNNRFIKVFWH 72

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 27 (RBM27); This subgroup corresponds to the RRM of RBM27 which contains a single RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although the specific function of the RRM in RBM27 remains unclear, it shows high sequence similarity with RRM1of RBM26, which functions as a cutaneous lymphoma (CL)-associated antigen.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAG--KLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWRK 248
Cdd:cd12517     1 NTKLEVRKIPQELNNITQLNEHFSKFGTIVNIQVAFGGdpEAALIQYTTNEEARRAISSTEAVLNNRFIRVLWHR 75

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1078654864  178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV---NFAGKL---AEIEFSTTAEAKNAYKS-PETIFDNRFVKV 244
Cdd:smart00360   1 TLFVGNLPPD-TTEEELRELFSKFGKVESVRLvrdKETGKSkgfAFVEFESEEDAEKALEAlNGKELDGRPLKV 73

RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins; This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1078654864 178 KLVVEKIPDDYCSEQaVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDNR 240
Cdd:cd12292     3 ILKITGIGPSVSRDD-LKELFKQFGEVEYVDFTPGDDEGHVRFKTSEAAQKARDAYTGKLELN 64

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 1078654864 178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV--NFAGKL---AEIEFSTTAEAKNAYK-SPETIFDNRFVKVYW 246
Cdd:cd12414     1 RLIVRNLPFK-CTEDDLKKLFSKFGKVLEVTIpkKPDGKLrgfAFVQFTNVADAAKAIKgMNGKKIKGRPVAVDW 74

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1078654864 179 LVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDN-RFVKVYWRK 248
Cdd:cd12443     3 IVCKNIPEELNDKEILRRHFSKFGKVARVFCNPRKNLAIVHFKDHESAALAKKKGKLLSKGgKPIEIFWSS 73

Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organizms from protists to humans. They are centred by precisely organized, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1078654864 255 ENEVAEQQRLQEERQAAFEEKEQRRKEHLEKmtgiLAQKKQLLE 298
Cdd:pfam06098 170 NAELAEVQRLEEQERRLREEKERRIAQQREA----LKKEKETAE 209

RNA recognition motif 3 (RRM3) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM3 of MRD1 which 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). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1078654864 190 SEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKS 232
Cdd:cd12568    13 TAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKA 55

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1078654864 178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKS 232
Cdd:cd12340     1 RLFVRPFPPD-TSESAIREIFSPYGPVKEVKMLSDSNFAFVEFEELEDAIRAKDS 54