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Protein

RNA-binding protein 5

Gene

RBM5

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the spliceosome A complex. Regulates alternative splicing of a number of mRNAs. May modulate splice site pairing after recruitment of the U1 and U2 snRNPs to the 5' and 3' splice sites of the intron. May both positively and negatively regulate apoptosis by regulating the alternative splicing of several genes involved in this process, including FAS and CASP2/caspase-2. In the case of FAS, promotes exclusion of exon 6 thereby producing a soluble form of FAS that inhibits apoptosis. In the case of CASP2/caspase-2, promotes exclusion of exon 9 thereby producing a catalytically active form of CASP2/Caspase-2 that induces apoptosis.7 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri181 – 210RanBP2-typePROSITE-ProRule annotationAdd BLAST30
Zinc fingeri647 – 677C2H2-type; atypicalPROSITE-ProRule annotationAdd BLAST31

GO - Molecular functioni

  • DNA binding Source: ProtInc
  • mRNA binding Source: UniProtKB
  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: ProtInc
  • zinc ion binding Source: InterPro

GO - Biological processi

  • apoptotic process Source: UniProtKB-KW
  • mRNA splicing, via spliceosome Source: Reactome
  • negative regulation of cell proliferation Source: UniProtKB
  • positive regulation of apoptotic process Source: UniProtKB
  • regulation of alternative mRNA splicing, via spliceosome Source: UniProtKB
  • RNA processing Source: ProtInc
  • spliceosomal complex assembly Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Apoptosis, mRNA processing, mRNA splicing

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000003756-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 5
Alternative name(s):
Protein G15
Putative tumor suppressor LUCA15
RNA-binding motif protein 5
Renal carcinoma antigen NY-REN-9
Gene namesi
Name:RBM5
ORF Names:H37, LUCA15
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:9902. RBM5.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • spliceosomal complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi10181.
OpenTargetsiENSG00000003756.
PharmGKBiPA34267.

Polymorphism and mutation databases

BioMutaiRBM5.
DMDMi13124794.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000817591 – 815RNA-binding protein 5Add BLAST815

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei18PhosphoserineCombined sources1
Modified residuei59PhosphoserineCombined sources1
Modified residuei69PhosphoserineCombined sources1
Modified residuei72PhosphoserineCombined sources1
Modified residuei78PhosphoserineCombined sources1
Modified residuei444PhosphoserineCombined sources1
Modified residuei621PhosphoserineCombined sources1
Modified residuei624PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP52756.
MaxQBiP52756.
PaxDbiP52756.
PeptideAtlasiP52756.
PRIDEiP52756.

PTM databases

iPTMnetiP52756.
PhosphoSitePlusiP52756.

Expressioni

Tissue specificityi

Isoform 5 is widely expressed in normal tissues and is expressed at increased levels in T-leukemic cell lines.

Gene expression databases

BgeeiENSG00000003756.
ExpressionAtlasiP52756. baseline and differential.
GenevisibleiP52756. HS.

Organism-specific databases

HPAiHPA017335.
HPA018011.

Interactioni

Subunit structurei

Component of the spliceosome A complex (also known as the prespliceosome). Appears to dissociate from the spliceosome upon formation of the spliceosome B complex (also known as the precatalytic spliceosome), in which the heterotrimeric U4/U6.U5 snRNPs are bound. Interacts with U2AF2; this interaction is direct. Also interacts with ACIN1, PRPF8, SFRS3, SNRPB, SNRPN, SNRNP70 and SNRNP200; these interactions may be indirect.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DHX15O4314315EBI-714003,EBI-1237044
PRPF19Q9UMS48EBI-714003,EBI-395746
U2AF2P263682EBI-714003,EBI-742339
U2SURPO150422EBI-714003,EBI-310697

Protein-protein interaction databases

BioGridi115480. 38 interactors.
DIPiDIP-47277N.
IntActiP52756. 26 interactors.
MINTiMINT-1406668.
STRINGi9606.ENSP00000343054.

Structurei

Secondary structure

1815
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi183 – 186Combined sources4
Turni188 – 190Combined sources3
Beta strandi193 – 195Combined sources3
Turni202 – 204Combined sources3
Beta strandi232 – 237Combined sources6
Helixi244 – 250Combined sources7
Turni252 – 254Combined sources3
Helixi259 – 261Combined sources3
Beta strandi268 – 272Combined sources5
Beta strandi274 – 280Combined sources7
Beta strandi282 – 284Combined sources3
Helixi285 – 295Combined sources11
Beta strandi296 – 299Combined sources4
Beta strandi301 – 303Combined sources3
Beta strandi306 – 312Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LK0NMR-A181-210[»]
2LK1NMR-A181-210[»]
2LKZNMR-A231-316[»]
ProteinModelPortaliP52756.
SMRiP52756.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini98 – 178RRM 1PROSITE-ProRule annotationAdd BLAST81
Domaini231 – 315RRM 2PROSITE-ProRule annotationAdd BLAST85
Domaini743 – 789G-patchPROSITE-ProRule annotationAdd BLAST47

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni321 – 809Required for interaction with U2AF21 PublicationAdd BLAST489
Regioni452 – 535Sufficient for interaction with ACIN1, PRPF8, SFRS3, SNRPB, SNRPN, SNRNP70 and SNRNP2001 PublicationAdd BLAST84

Sequence similaritiesi

Belongs to the RBM5/RBM10 family.Curated
Contains 1 C2H2-type zinc finger.PROSITE-ProRule annotation
Contains 1 G-patch domain.PROSITE-ProRule annotation
Contains 1 RanBP2-type zinc finger.PROSITE-ProRule annotation
Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri181 – 210RanBP2-typePROSITE-ProRule annotationAdd BLAST30
Zinc fingeri647 – 677C2H2-type; atypicalPROSITE-ProRule annotationAdd BLAST31

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG0154. Eukaryota.
ENOG410YNFQ. LUCA.
GeneTreeiENSGT00510000046476.
HOVERGENiHBG000318.
InParanoidiP52756.
KOiK13094.
OMAiSALDGYG.
OrthoDBiEOG091G01UT.
PhylomeDBiP52756.
TreeFamiTF315789.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
4.10.1060.10. 1 hit.
InterProiIPR000467. G_patch_dom.
IPR012677. Nucleotide-bd_a/b_plait.
IPR033094. RBM5.
IPR000504. RRM_dom.
IPR007087. Znf_C2H2.
IPR001876. Znf_RanBP2.
[Graphical view]
PANTHERiPTHR13948:SF21. PTHR13948:SF21. 2 hits.
PfamiPF01585. G-patch. 1 hit.
PF00076. RRM_1. 1 hit.
PF00641. zf-RanBP. 1 hit.
[Graphical view]
SMARTiSM00443. G_patch. 1 hit.
SM00360. RRM. 2 hits.
SM00547. ZnF_RBZ. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
SSF90209. SSF90209. 1 hit.
PROSITEiPS50174. G_PATCH. 1 hit.
PS50102. RRM. 2 hits.
PS01358. ZF_RANBP2_1. 1 hit.
PS50199. ZF_RANBP2_2. 1 hit.
PS50157. ZINC_FINGER_C2H2_2. 1 hit.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P52756-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGSDKRVSRT ERSGRYGSII DRDDRDERES RSRRRDSDYK RSSDDRRGDR
60 70 80 90 100
YDDYRDYDSP ERERERRNSD RSEDGYHSDG DYGEHDYRHD ISDERESKTI
110 120 130 140 150
MLRGLPITIT ESDIREMMES FEGPQPADVR LMKRKTGVSR GFAFVEFYHL
160 170 180 190 200
QDATSWMEAN QKKLVIQGKH IAMHYSNPRP KFEDWLCNKC CLNNFRKRLK
210 220 230 240 250
CFRCGADKFD SEQEVPPGTT ESVQSVDYYC DTIILRNIAP HTVVDSIMTA
260 270 280 290 300
LSPYASLAVN NIRLIKDKQT QQNRGFAFVQ LSSAMDASQL LQILQSLHPP
310 320 330 340 350
LKIDGKTIGV DFAKSARKDL VLSDGNRVSA FSVASTAIAA AQWSSTQSQS
360 370 380 390 400
GEGGSVDYSY LQPGQDGYAQ YAQYSQDYQQ FYQQQAGGLE SDASSASGTA
410 420 430 440 450
VTTTSAAVVS QSPQLYNQTS NPPGSPTEEA QPSTSTSTQA PAASPTGVVP
460 470 480 490 500
GTKYAVPDTS TYQYDESSGY YYDPTTGLYY DPNSQYYYNS LTQQYLYWDG
510 520 530 540 550
EKETYVPAAE SSSHQQSGLP PAKEGKEKKE KPKSKTAQQI AKDMERWAKS
560 570 580 590 600
LNKQKENFKN SFQPVNSLRE EERRESAAAD AGFALFEKKG ALAERQQLIP
610 620 630 640 650
ELVRNGDEEN PLKRGLVAAY SGDSDNEEEL VERLESEEEK LADWKKMACL
660 670 680 690 700
LCRRQFPNKD ALVRHQQLSD LHKQNMDIYR RSRLSEQELE ALELREREMK
710 720 730 740 750
YRDRAAERRE KYGIPEPPEP KRKKQFDAGT VNYEQPTKDG IDHSNIGNKM
760 770 780 790 800
LQAMGWREGS GLGRKCQGIT APIEAQVRLK GAGLGAKGSA YGLSGADSYK
810
DAVRKAMFAR FTEME
Length:815
Mass (Da):92,154
Last modified:February 21, 2001 - v2
Checksum:iAA79962D13405479
GO
Isoform 2 (identifier: P52756-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     138-143: VSRGFA → ESLLSS
     144-815: Missing.

Show »
Length:143
Mass (Da):17,055
Checksum:i9D5FC205E7B15147
GO
Isoform 3 (identifier: P52756-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     65-126: ERRNSDRSED...MMESFEGPQP → YSRNDGVLRR...DSRKAHCNAL
     127-815: Missing.

Note: No experimental confirmation available.
Show »
Length:126
Mass (Da):14,897
Checksum:iDCF25D0B05DD2BF6
GO
Isoform 4 (identifier: P52756-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     142-815: Missing.

Note: No experimental confirmation available.
Show »
Length:141
Mass (Da):16,838
Checksum:i2D46C7A88147A429
GO
Isoform 5 (identifier: P52756-5) [UniParc]FASTAAdd to basket
Also known as: delta-6

The sequence of this isoform differs from the canonical sequence as follows:
     137-150: GVSRGFAFVEFYHL → EKVGDSRKAHCNAL
     151-815: Missing.

Show »
Length:150
Mass (Da):17,891
Checksum:iEC00925B099F81DC
GO

Sequence cautioni

The sequence BAG59728 differs from that shown. Reason: Erroneous translation. Wrong choice of CDS.Curated
The sequence BAG59871 differs from that shown. Reason: Erroneous translation. Wrong choice of CDS.Curated
The sequence BAG63975 differs from that shown. Reason: Erroneous translation. Wrong choice of CDS.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti53 – 54DY → GS in AAA99715 (Ref. 1) Curated2
Sequence conflicti354G → V in AAA99715 (Ref. 1) Curated1
Sequence conflicti455Missing in AAB42216 (Ref. 8) Curated1
Sequence conflicti788G → A in AAB42216 (Ref. 8) Curated1
Sequence conflicti812T → I in AAA99715 (Ref. 1) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_061831163K → N.Corresponds to variant rs56783610dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_03742965 – 126ERRNS…EGPQP → YSRNDGVLRRPSACGCEADE EENRCKPWFRLRGVLSLARC YQLDGSQSEKVGDSRKAHCN AL in isoform 3. 1 PublicationAdd BLAST62
Alternative sequenceiVSP_037430127 – 815Missing in isoform 3. 1 PublicationAdd BLAST689
Alternative sequenceiVSP_037431137 – 150GVSRG…EFYHL → EKVGDSRKAHCNAL in isoform 5. 1 PublicationAdd BLAST14
Alternative sequenceiVSP_037432138 – 143VSRGFA → ESLLSS in isoform 2. 1 Publication6
Alternative sequenceiVSP_037433142 – 815Missing in isoform 4. 1 PublicationAdd BLAST674
Alternative sequenceiVSP_037434144 – 815Missing in isoform 2. 1 PublicationAdd BLAST672
Alternative sequenceiVSP_037435151 – 815Missing in isoform 5. 1 PublicationAdd BLAST665

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U23946 mRNA. Translation: AAA99715.1.
AF091263 mRNA. Translation: AAD04159.1.
AF103802 mRNA. Translation: AAF02422.2.
AF107493 mRNA. Translation: AAF99551.1.
AK297249 mRNA. Translation: BAG59728.1. Sequence problems.
AK297445 mRNA. Translation: BAG59871.1. Sequence problems.
AK302766 mRNA. Translation: BAG63975.1. Sequence problems.
AK314032 mRNA. Translation: BAG36742.1.
CH471055 Genomic DNA. Translation: EAW65040.1.
CH471055 Genomic DNA. Translation: EAW65041.1.
U73168 Genomic DNA. Translation: AAB42216.1.
CCDSiCCDS2810.1. [P52756-1]
RefSeqiNP_005769.1. NM_005778.3. [P52756-1]
XP_016860992.1. XM_017005503.1. [P52756-1]
UniGeneiHs.439480.

Genome annotation databases

EnsembliENST00000347869; ENSP00000343054; ENSG00000003756. [P52756-1]
ENST00000469838; ENSP00000419534; ENSG00000003756. [P52756-2]
GeneIDi10181.
KEGGihsa:10181.
UCSCiuc003cyf.4. human. [P52756-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U23946 mRNA. Translation: AAA99715.1.
AF091263 mRNA. Translation: AAD04159.1.
AF103802 mRNA. Translation: AAF02422.2.
AF107493 mRNA. Translation: AAF99551.1.
AK297249 mRNA. Translation: BAG59728.1. Sequence problems.
AK297445 mRNA. Translation: BAG59871.1. Sequence problems.
AK302766 mRNA. Translation: BAG63975.1. Sequence problems.
AK314032 mRNA. Translation: BAG36742.1.
CH471055 Genomic DNA. Translation: EAW65040.1.
CH471055 Genomic DNA. Translation: EAW65041.1.
U73168 Genomic DNA. Translation: AAB42216.1.
CCDSiCCDS2810.1. [P52756-1]
RefSeqiNP_005769.1. NM_005778.3. [P52756-1]
XP_016860992.1. XM_017005503.1. [P52756-1]
UniGeneiHs.439480.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LK0NMR-A181-210[»]
2LK1NMR-A181-210[»]
2LKZNMR-A231-316[»]
ProteinModelPortaliP52756.
SMRiP52756.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115480. 38 interactors.
DIPiDIP-47277N.
IntActiP52756. 26 interactors.
MINTiMINT-1406668.
STRINGi9606.ENSP00000343054.

PTM databases

iPTMnetiP52756.
PhosphoSitePlusiP52756.

Polymorphism and mutation databases

BioMutaiRBM5.
DMDMi13124794.

Proteomic databases

EPDiP52756.
MaxQBiP52756.
PaxDbiP52756.
PeptideAtlasiP52756.
PRIDEiP52756.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000347869; ENSP00000343054; ENSG00000003756. [P52756-1]
ENST00000469838; ENSP00000419534; ENSG00000003756. [P52756-2]
GeneIDi10181.
KEGGihsa:10181.
UCSCiuc003cyf.4. human. [P52756-1]

Organism-specific databases

CTDi10181.
DisGeNETi10181.
GeneCardsiRBM5.
HGNCiHGNC:9902. RBM5.
HPAiHPA017335.
HPA018011.
MIMi606884. gene.
neXtProtiNX_P52756.
OpenTargetsiENSG00000003756.
PharmGKBiPA34267.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0154. Eukaryota.
ENOG410YNFQ. LUCA.
GeneTreeiENSGT00510000046476.
HOVERGENiHBG000318.
InParanoidiP52756.
KOiK13094.
OMAiSALDGYG.
OrthoDBiEOG091G01UT.
PhylomeDBiP52756.
TreeFamiTF315789.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000003756-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.

Miscellaneous databases

ChiTaRSiRBM5. human.
GeneWikiiRBM5.
GenomeRNAii10181.
PROiP52756.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000003756.
ExpressionAtlasiP52756. baseline and differential.
GenevisibleiP52756. HS.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
4.10.1060.10. 1 hit.
InterProiIPR000467. G_patch_dom.
IPR012677. Nucleotide-bd_a/b_plait.
IPR033094. RBM5.
IPR000504. RRM_dom.
IPR007087. Znf_C2H2.
IPR001876. Znf_RanBP2.
[Graphical view]
PANTHERiPTHR13948:SF21. PTHR13948:SF21. 2 hits.
PfamiPF01585. G-patch. 1 hit.
PF00076. RRM_1. 1 hit.
PF00641. zf-RanBP. 1 hit.
[Graphical view]
SMARTiSM00443. G_patch. 1 hit.
SM00360. RRM. 2 hits.
SM00547. ZnF_RBZ. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
SSF90209. SSF90209. 1 hit.
PROSITEiPS50174. G_PATCH. 1 hit.
PS50102. RRM. 2 hits.
PS01358. ZF_RANBP2_1. 1 hit.
PS50199. ZF_RANBP2_2. 1 hit.
PS50157. ZINC_FINGER_C2H2_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRBM5_HUMAN
AccessioniPrimary (citable) accession number: P52756
Secondary accession number(s): B2RA45
, B4DM16, B4DMF9, B4DZ63, Q93021, Q9BU14, Q9HDA6, Q9UKY8, Q9UL24
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: February 21, 2001
Last modified: November 2, 2016
This is version 163 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.