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Protein

RNA-binding protein 25

Gene

RBM25

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

Functioni

RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5'-splice site (5'-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5'-ss usage through the 5'-CGGGCA-3' RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5' ss in a 5'-CGGGCA-3'-dependent manner. Binds to the exonic splicing enhancer 5'-CGGGCA-3' RNA sequence located within exon 2 of the BCL2L1 pre-mRNA. Also involved in the generation of an abnormal and truncated splice form of SCN5A in heart failure.2 Publications

GO - Molecular functioni

  • mRNA binding Source: UniProtKB
  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • regulation of alternative mRNA splicing, via spliceosome Source: UniProtKB
  • regulation of apoptotic process Source: UniProtKB
  • RNA splicing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 25
Alternative name(s):
Arg/Glu/Asp-rich protein of 120 kDa
Short name:
RED120
Protein S164
RNA-binding motif protein 25
RNA-binding region-containing protein 7
Gene namesi
Name:RBM25
Synonyms:RNPC7
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 14

Organism-specific databases

HGNCiHGNC:23244. RBM25.

Subcellular locationi

  • Nucleus speckle
  • Cytoplasm

  • Note: Colocalizes predominantly, with SFRS2 and LUC7L3 splicing factors, in nuclear speckles. Cytoplasmic localization is faint.

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nuclear speck Source: UniProtKB
  • nucleoplasm Source: HPA
  • spliceosomal complex Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi734 – 736KRK → AAA: Reduced DNA/RNA binding. 1 Publication3
Mutagenesisi777 – 778KK → AA: Reduced DNA/RNA binding. 1 Publication2
Mutagenesisi825K → A: Reduced DNA/RNA binding; when associated with A-828. 1 Publication1
Mutagenesisi828R → A: Reduced DNA/RNA binding; when associated with A-825. 1 Publication1

Organism-specific databases

DisGeNETi58517.
OpenTargetsiENSG00000119707.
PharmGKBiPA134912024.

Polymorphism and mutation databases

BioMutaiRBM25.
DMDMi226693631.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000817841 – 843RNA-binding protein 25Add BLAST843

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei135N6-acetyllysineBy similarity1
Modified residuei226PhosphoserineCombined sources1
Modified residuei229PhosphoserineCombined sources1
Cross-linki273Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki578Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei583PhosphoserineCombined sources1
Modified residuei677PhosphoserineCombined sources1 Publication1
Modified residuei683PhosphoserineCombined sources1
Modified residuei703PhosphoserineCombined sources1

Post-translational modificationi

Sumoylated.1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP49756.
MaxQBiP49756.
PaxDbiP49756.
PeptideAtlasiP49756.
PRIDEiP49756.

PTM databases

iPTMnetiP49756.
PhosphoSitePlusiP49756.
SwissPalmiP49756.

Expressioni

Gene expression databases

BgeeiENSG00000119707.
CleanExiHS_RBM25.
ExpressionAtlasiP49756. baseline and differential.
GenevisibleiP49756. HS.

Organism-specific databases

HPAiHPA003025.

Interactioni

Subunit structurei

Interacts with LUC7L3 and SRRM1. Specifically associates with functional splicing complexes, including Sm proteins and U1, U2, U4, U5 and U6 snRNAs. Associates with exon junction complex (EJC) proteins, including APEX1, BAT1, NCBP1, RBM8A and RNPS1. Interaction with NCBP1 is RNA-dependent.2 Publications

Protein-protein interaction databases

BioGridi121843. 76 interactors.
IntActiP49756. 27 interactors.
MINTiMINT-4545359.
STRINGi9606.ENSP00000261973.

Structurei

Secondary structure

1843
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi739 – 744Combined sources6
Helixi749 – 754Combined sources6
Turni759 – 761Combined sources3
Helixi764 – 769Combined sources6
Helixi771 – 782Combined sources12
Helixi789 – 799Combined sources11
Helixi804 – 815Combined sources12
Helixi818 – 839Combined sources22

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3V53X-ray2.90A/B/C/D/E734-843[»]
ProteinModelPortaliP49756.
SMRiP49756.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini87 – 164RRMPROSITE-ProRule annotationAdd BLAST78
Domaini750 – 843PWIPROSITE-ProRule annotationAdd BLAST94

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni285 – 644Necessary for nuclear speckle localizationAdd BLAST360

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi292 – 608Glu-richAdd BLAST317
Compositional biasi309 – 549Arg-richAdd BLAST241

Domaini

The PWI domain binds nucleic acids with significant help from its N-terminal flanking basic region. It has an equal preference for binding to single- or double-stranded species, and it contributes to RBM25 role in modulation of alternative splicing, maybe by mediating RNA-dependent association with LUC7L3.

Sequence similaritiesi

Contains 1 PWI domain.PROSITE-ProRule annotation
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2253. Eukaryota.
ENOG410ZRGA. LUCA.
GeneTreeiENSGT00730000111019.
HOVERGENiHBG068941.
InParanoidiP49756.
KOiK12822.
OMAiTWREKEM.
OrthoDBiEOG091G05NK.
PhylomeDBiP49756.
TreeFamiTF320185.

Family and domain databases

Gene3Di1.20.1390.10. 1 hit.
3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR002483. PWI_dom.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF01480. PWI. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00311. PWI. 1 hit.
SM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF101233. SSF101233. 1 hit.
SSF54928. SSF54928. 1 hit.
PROSITEiPS51025. PWI. 1 hit.
PS50102. RRM. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P49756-1) [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
MSFPPHLNRP PMGIPALPPG IPPPQFPGFP PPVPPGTPMI PVPMSIMAPA
60 70 80 90 100
PTVLVPTVSM VGKHLGARKD HPGLKAKEND ENCGPTTTVF VGNISEKASD
110 120 130 140 150
MLIRQLLAKC GLVLSWKRVQ GASGKLQAFG FCEYKEPEST LRALRLLHDL
160 170 180 190 200
QIGEKKLLVK VDAKTKAQLD EWKAKKKASN GNARPETVTN DDEEALDEET
210 220 230 240 250
KRRDQMIKGA IEVLIREYSS ELNAPSQESD SHPRKKKKEK KEDIFRRFPV
260 270 280 290 300
APLIPYPLIT KEDINAIEME EDKRDLISRE ISKFRDTHKK LEEEKGKKEK
310 320 330 340 350
ERQEIEKERR ERERERERER ERRERERERE REREREKEKE RERERERDRD
360 370 380 390 400
RDRTKERDRD RDRERDRDRD RERSSDRNKD RSRSREKSRD RERERERERE
410 420 430 440 450
RERERERERE RERERERERE REREREKDKK RDREEDEEDA YERRKLERKL
460 470 480 490 500
REKEAAYQER LKNWEIRERK KTREYEKEAE REEERRREMA KEAKRLKEFL
510 520 530 540 550
EDYDDDRDDP KYYRGSALQK RLRDREKEME ADERDRKREK EELEEIRQRL
560 570 580 590 600
LAEGHPDPDA ELQRMEQEAE RRRQPQIKQE PESEEEEEEK QEKEEKREEP
610 620 630 640 650
MEEEEEPEQK PCLKPTLRPI SSAPSVSSAS GNATPNTPGD ESPCGIIIPH
660 670 680 690 700
ENSPDQQQPE EHRPKIGLSL KLGASNSPGQ PNSVKRKKLP VDSVFNKFED
710 720 730 740 750
EDSDDVPRKR KLVPLDYGED DKNATKGTVN TEEKRKHIKS LIEKIPTAKP
760 770 780 790 800
ELFAYPLDWS IVDSILMERR IRPWINKKII EYIGEEEATL VDFVCSKVMA
810 820 830 840
HSSPQSILDD VAMVLDEEAE VFIVKMWRLL IYETEAKKIG LVK
Length:843
Mass (Da):100,185
Last modified:April 14, 2009 - v3
Checksum:i80534590147A342A
GO
Isoform 2 (identifier: P49756-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     290-294: KLEEE → RSYGD
     295-843: Missing.

Note: No experimental confirmation available.
Show »
Length:294
Mass (Da):32,822
Checksum:i184FE9019A3E3D95
GO
Isoform 3 (identifier: P49756-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     290-300: KLEEEKGKKEK → VVFLSFHLIPI
     301-843: Missing.

Show »
Length:300
Mass (Da):33,510
Checksum:i81D1498626DDD750
GO
Isoform 4 (identifier: P49756-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     109-164: KCGLVLSWKR...KKLLVKVDAK → PSDSVSTRSQ...QRRKLLMGLG
     165-843: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Show »
Length:164
Mass (Da):17,953
Checksum:i5D5562C8AAD78BAE
GO

Sequence cautioni

The sequence AAH62440 differs from that shown. Contaminating sequence. Potential poly-A sequence.Curated
The sequence AAH62440 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAH83496 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAG52915 differs from that shown. Reason: Erroneous translation. Wrong choice of CDS.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti428D → K in BAB15362 (PubMed:14702039).Curated1
Sequence conflicti571 – 574RRRQ → EAQE in AAC41999 (PubMed:7596406).Curated4

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_039881109 – 164KCGLV…KVDAK → PSDSVSTRSQNLPSVHSDYY MTCKLERKSYSLKLMQRQRH SWMNGKQRRKLLMGLG in isoform 4. 1 PublicationAdd BLAST56
Alternative sequenceiVSP_039882165 – 843Missing in isoform 4. 1 PublicationAdd BLAST679
Alternative sequenceiVSP_036791290 – 300KLEEEKGKKEK → VVFLSFHLIPI in isoform 3. 1 PublicationAdd BLAST11
Alternative sequenceiVSP_036792290 – 294KLEEE → RSYGD in isoform 2. 1 Publication5
Alternative sequenceiVSP_036793295 – 843Missing in isoform 2. 1 PublicationAdd BLAST549
Alternative sequenceiVSP_036794301 – 843Missing in isoform 3. 1 PublicationAdd BLAST543

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK026107 mRNA. Translation: BAB15362.1.
AK094697 mRNA. Translation: BAG52915.1. Sequence problems.
AL442663 Genomic DNA. No translation available.
AC004858 Genomic DNA. Translation: AAF19255.1.
CH471061 Genomic DNA. Translation: EAW81087.1.
BC062440 mRNA. Translation: AAH62440.1. Sequence problems.
BC083496 mRNA. Translation: AAH83496.1. Different initiation.
BC111066 mRNA. Translation: AAI11067.1.
BC113389 mRNA. Translation: AAI13390.1.
BC113391 mRNA. Translation: AAI13392.1.
BC136775 mRNA. Translation: AAI36776.1.
BC136776 mRNA. Translation: AAI36777.1.
BC144407 mRNA. Translation: AAI44408.1.
AF109907 Genomic DNA. Translation: AAC97961.1.
L40392 mRNA. Translation: AAC41999.1.
CCDSiCCDS32113.1. [P49756-1]
RefSeqiNP_067062.1. NM_021239.2. [P49756-1]
XP_011535346.1. XM_011537044.2. [P49756-1]
XP_011535347.1. XM_011537045.2.
UniGeneiHs.531106.

Genome annotation databases

EnsembliENST00000261973; ENSP00000261973; ENSG00000119707. [P49756-1]
ENST00000525321; ENSP00000436868; ENSG00000119707. [P49756-3]
ENST00000526754; ENSP00000436225; ENSG00000119707. [P49756-2]
ENST00000527432; ENSP00000431150; ENSG00000119707. [P49756-1]
ENST00000528081; ENSP00000434444; ENSG00000119707. [P49756-4]
GeneIDi58517.
KEGGihsa:58517.
UCSCiuc001xnn.5. human. [P49756-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK026107 mRNA. Translation: BAB15362.1.
AK094697 mRNA. Translation: BAG52915.1. Sequence problems.
AL442663 Genomic DNA. No translation available.
AC004858 Genomic DNA. Translation: AAF19255.1.
CH471061 Genomic DNA. Translation: EAW81087.1.
BC062440 mRNA. Translation: AAH62440.1. Sequence problems.
BC083496 mRNA. Translation: AAH83496.1. Different initiation.
BC111066 mRNA. Translation: AAI11067.1.
BC113389 mRNA. Translation: AAI13390.1.
BC113391 mRNA. Translation: AAI13392.1.
BC136775 mRNA. Translation: AAI36776.1.
BC136776 mRNA. Translation: AAI36777.1.
BC144407 mRNA. Translation: AAI44408.1.
AF109907 Genomic DNA. Translation: AAC97961.1.
L40392 mRNA. Translation: AAC41999.1.
CCDSiCCDS32113.1. [P49756-1]
RefSeqiNP_067062.1. NM_021239.2. [P49756-1]
XP_011535346.1. XM_011537044.2. [P49756-1]
XP_011535347.1. XM_011537045.2.
UniGeneiHs.531106.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3V53X-ray2.90A/B/C/D/E734-843[»]
ProteinModelPortaliP49756.
SMRiP49756.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121843. 76 interactors.
IntActiP49756. 27 interactors.
MINTiMINT-4545359.
STRINGi9606.ENSP00000261973.

PTM databases

iPTMnetiP49756.
PhosphoSitePlusiP49756.
SwissPalmiP49756.

Polymorphism and mutation databases

BioMutaiRBM25.
DMDMi226693631.

Proteomic databases

EPDiP49756.
MaxQBiP49756.
PaxDbiP49756.
PeptideAtlasiP49756.
PRIDEiP49756.

Protocols and materials databases

DNASUi58517.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000261973; ENSP00000261973; ENSG00000119707. [P49756-1]
ENST00000525321; ENSP00000436868; ENSG00000119707. [P49756-3]
ENST00000526754; ENSP00000436225; ENSG00000119707. [P49756-2]
ENST00000527432; ENSP00000431150; ENSG00000119707. [P49756-1]
ENST00000528081; ENSP00000434444; ENSG00000119707. [P49756-4]
GeneIDi58517.
KEGGihsa:58517.
UCSCiuc001xnn.5. human. [P49756-1]

Organism-specific databases

CTDi58517.
DisGeNETi58517.
GeneCardsiRBM25.
HGNCiHGNC:23244. RBM25.
HPAiHPA003025.
MIMi612427. gene.
neXtProtiNX_P49756.
OpenTargetsiENSG00000119707.
PharmGKBiPA134912024.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2253. Eukaryota.
ENOG410ZRGA. LUCA.
GeneTreeiENSGT00730000111019.
HOVERGENiHBG068941.
InParanoidiP49756.
KOiK12822.
OMAiTWREKEM.
OrthoDBiEOG091G05NK.
PhylomeDBiP49756.
TreeFamiTF320185.

Miscellaneous databases

ChiTaRSiRBM25. human.
GeneWikiiRBM25.
GenomeRNAii58517.
PROiP49756.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000119707.
CleanExiHS_RBM25.
ExpressionAtlasiP49756. baseline and differential.
GenevisibleiP49756. HS.

Family and domain databases

Gene3Di1.20.1390.10. 1 hit.
3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR002483. PWI_dom.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF01480. PWI. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00311. PWI. 1 hit.
SM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF101233. SSF101233. 1 hit.
SSF54928. SSF54928. 1 hit.
PROSITEiPS51025. PWI. 1 hit.
PS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRBM25_HUMAN
AccessioniPrimary (citable) accession number: P49756
Secondary accession number(s): A0PJL9
, B2RNA8, B3KT03, Q2TA72, Q5XJ17, Q6P665, Q9H6A1, Q9UEQ5, Q9UIE9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: April 14, 2009
Last modified: November 30, 2016
This is version 139 of the entry and version 3 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 14
    Human chromosome 14: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.