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Conserved domains on  [gi|42569396|ref|NP_180347|]
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RNA-binding (RRM/RBD/RNP motifs) family protein [Arabidopsis thaliana]

Protein Classification

RNA-binding protein 48( domain architecture ID 10189584)

RNA-binding protein 48 (RBM48) is essential for the splicing of U12-type introns in both plants and animals

Gene Ontology:  GO:0003723
PubMed:  15853797|22278943|18515081
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_RBM48 cd12442
RNA recognition motif (RRM) found in RNA-binding protein 48 (RBM48) and similar proteins; This ...
 11-110 3.14e-61

RNA recognition motif (RRM) found in RNA-binding protein 48 (RBM48) and similar proteins; This subfamily corresponds to the RRM of RBM48, a putative RNA-binding protein of unknown function. It contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


:

Pssm-ID: 409876 [Multi-domain]  Cd Length: 100  Bit Score: 187.42  E-value: 3.14e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569396  11 VRVYTVCDESRYMIVRNVPALGCGDDLMRLFMTYGEVEECKPMDAEDCAEFTDVYWIKFRLITNARFAKRKLDESSFLGN 90
Cdd:cd12442   1 VKVYTVNQESRYLLVQGVPALGVEEELLKLFSLYGTIEEYRILDEYPCEEFTEVYLIKFERIQSARFAKRKLDDHSFFGG 80

                        90       100
                ....*....|....*....|
gi 42569396  91 RLQISYAPEYENVNDTKDKL 110
Cdd:cd12442  81 ILHVCYAPEYETVEDTREKL 100
 
Name Accession Description Interval E-value
RRM_RBM48 cd12442
RNA recognition motif (RRM) found in RNA-binding protein 48 (RBM48) and similar proteins; This ...
 11-110 3.14e-61

RNA recognition motif (RRM) found in RNA-binding protein 48 (RBM48) and similar proteins; This subfamily corresponds to the RRM of RBM48, a putative RNA-binding protein of unknown function. It contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409876 [Multi-domain]  Cd Length: 100  Bit Score: 187.42  E-value: 3.14e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569396  11 VRVYTVCDESRYMIVRNVPALGCGDDLMRLFMTYGEVEECKPMDAEDCAEFTDVYWIKFRLITNARFAKRKLDESSFLGN 90
Cdd:cd12442   1 VKVYTVNQESRYLLVQGVPALGVEEELLKLFSLYGTIEEYRILDEYPCEEFTEVYLIKFERIQSARFAKRKLDDHSFFGG 80

                        90       100
                ....*....|....*....|
gi 42569396  91 RLQISYAPEYENVNDTKDKL 110
Cdd:cd12442  81 ILHVCYAPEYETVEDTREKL 100
 
Name Accession Description Interval E-value
RRM_RBM48 cd12442
RNA recognition motif (RRM) found in RNA-binding protein 48 (RBM48) and similar proteins; This ...
 11-110 3.14e-61

RNA recognition motif (RRM) found in RNA-binding protein 48 (RBM48) and similar proteins; This subfamily corresponds to the RRM of RBM48, a putative RNA-binding protein of unknown function. It contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409876 [Multi-domain]  Cd Length: 100  Bit Score: 187.42  E-value: 3.14e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569396  11 VRVYTVCDESRYMIVRNVPALGCGDDLMRLFMTYGEVEECKPMDAEDCAEFTDVYWIKFRLITNARFAKRKLDESSFLGN 90
Cdd:cd12442   1 VKVYTVNQESRYLLVQGVPALGVEEELLKLFSLYGTIEEYRILDEYPCEEFTEVYLIKFERIQSARFAKRKLDDHSFFGG 80

                        90       100
                ....*....|....*....|
gi 42569396  91 RLQISYAPEYENVNDTKDKL 110
Cdd:cd12442  81 ILHVCYAPEYETVEDTREKL 100
RRM2_VICKZ cd12359
RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds ...
 21-99 7.66e-04

RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 409794 [Multi-domain]  Cd Length: 76  Bit Score: 37.35  E-value: 7.66e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569396  21 RYMIVRNVPALGCGDDLMRLFMTYGEVEECK--PMDAEdcaefTDVYWIKFRLITNARFAKRKLDESSFLGNRLQISYAP 98
Cdd:cd12359   1 RKIQIRNIPPHARWEDLDSLLSTYGTVENCEqvNTKSE-----TATVNVTYESPEQAQQAVNKLNGYQYEGSALKVSYIP 75


                .
gi 42569396  99 E 99
Cdd:cd12359  76 D 76
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 24-95 8.14e-04

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: 36.88  E-value: 8.14e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42569396  24 IVRNVPALGCGDDLMRLFMTYGEVEECKPMDAEDCaEFTDVYWIKFRLITNARFAKRKLDESSFLGNRLQIS 95
Cdd:cd00590   2 FVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDG-KSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 25-94 1.46e-03

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.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 36.55  E-value: 1.46e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42569396  25 VRNVPALGCGDDLMRLFMTYGEVEECK-PMDAEDCAEfTDVYWIKFRLITNARFAKRKLDESSFLGNRLQI 94
Cdd:cd12316   4 VRNLPFTATEDELRELFEAFGKISEVHiPLDKQTKRS-KGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHV 73
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
 25-97 7.43e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 34.66  E-value: 7.43e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 42569396  25 VRNVPALGCGDDLMRLFMTYGEVEECK-PMDAEDCAEFTDVYwIKFRLITNARFAKRKLDESSFLGNRLQISYA 97
Cdd:cd12312   5 VRNVADDTRPDDLRREFGRYGPIVDVYiPLDFYTRRPRGFAY-IQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 40-97 7.82e-03

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 34.43  E-value: 7.82e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42569396  40 LFMTYGEVEE---CKPMDAEDCAeftdvyWIKFRLITNARFAKRKLDESSFLGNRLQISYA 97
Cdd:cd12246  23 LFSQFGPVLDivaSKSLKMRGQA------FVVFKDVESATNALRALQGFPFYGKPMRIQYA 77
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
 19-97 8.96e-03

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410186 [Multi-domain]  Cd Length: 79  Bit Score: 34.22  E-value: 8.96e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42569396  19 ESRYMIVRNVPALGCGDDLMRLFMTYGEVEECKPMDAEDcAEFTDVYWIKFRLITNARFAKRKLDESSFLGNRLQISYA 97
Cdd:cd21607   1 RNNTIYCSNLPLSTAESDLYDLFETIGKVNNAELKYDET-GDPTGSAVVEYENLDDADVCISKLNNYNYGGCDLKISYA 78
 
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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