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Protein

RNA-binding protein 40

Gene

RNPC3

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

Functioni

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3'-stem-loop of m7G-capped U12 snRNA.2 Publications

GO - Molecular functioni

GO - Biological processi

  • developmental process Source: GO_Central
  • mRNA splicing, via spliceosome Source: GO_Central
  • RNA splicing Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 40
Alternative name(s):
RNA-binding motif protein 40
RNA-binding region-containing protein 3
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
Short name:
U11/U12 snRNP 65 kDa protein
Short name:
U11/U12-65K
Gene namesi
Name:RNPC3
Synonyms:KIAA1839, RBM40, RNP
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:18666. RNPC3.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: HPA
  • nucleus Source: MGI
  • U12-type spliceosomal complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

MalaCardsiRNPC3.
Orphaneti231662. Isolated growth hormone deficiency type IA.
PharmGKBiPA134865246.

Polymorphism and mutation databases

BioMutaiRNPC3.
DMDMi74760946.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 517517RNA-binding protein 40PRO_0000311112Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei21 – 211PhosphoserineCombined sources
Modified residuei108 – 1081PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ96LT9.
MaxQBiQ96LT9.
PaxDbiQ96LT9.
PeptideAtlasiQ96LT9.
PRIDEiQ96LT9.

PTM databases

iPTMnetiQ96LT9.
PhosphoSiteiQ96LT9.

Expressioni

Tissue specificityi

Highly expressed in pancreas and kidney. Detected at lower levels in heart, brain, placenta, lung, liver, spleen, thymus, prostate, testis, ovary, small intestine, colon and leukocytes.1 Publication

Gene expression databases

BgeeiENSG00000185946.
CleanExiHS_RNPC3.
ExpressionAtlasiQ96LT9. baseline and differential.
GenevisibleiQ96LT9. HS.

Organism-specific databases

HPAiHPA052434.

Interactioni

Subunit structurei

Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Found in a complex with m7G-capped U12 snRNA. Interacts with PDCD7.3 Publications

Protein-protein interaction databases

BioGridi120740. 19 interactions.
IntActiQ96LT9. 6 interactions.
MINTiMINT-1180654.
STRINGi9606.ENSP00000391432.

Structurei

Secondary structure

1
517
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi391 – 3977Combined sources
Helixi401 – 4066Combined sources
Helixi408 – 4103Combined sources
Beta strandi420 – 4278Combined sources
Helixi433 – 4408Combined sources
Helixi441 – 4433Combined sources
Helixi449 – 4546Combined sources
Beta strandi456 – 4627Combined sources
Turni463 – 4653Combined sources
Beta strandi466 – 4727Combined sources
Helixi476 – 48611Combined sources
Beta strandi489 – 4913Combined sources
Beta strandi497 – 5004Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EGNX-ray2.50A380-517[»]
ProteinModelPortaliQ96LT9.
SMRiQ96LT9. Positions 24-103, 387-506.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96LT9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini27 – 10276RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini420 – 50384RRM 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 257257Necessary for interaction with PDCD7Add
BLAST
Regioni211 – 380170Necessary for binding to m(7)G-capped U12 snRNAAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi196 – 23338Pro-richAdd
BLAST

Sequence similaritiesi

Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG4206. Eukaryota.
ENOG410XQEY. LUCA.
GeneTreeiENSGT00530000063786.
HOGENOMiHOG000007217.
HOVERGENiHBG057088.
InParanoidiQ96LT9.
KOiK13157.
OMAiEDRQRMN.
OrthoDBiEOG091G0OCH.
PhylomeDBiQ96LT9.
TreeFamiTF324298.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96LT9-1) [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
MAAPEQPLAI SRGCTSSSSL SPPRGDRTLL VRHLPAELTA EEKEDLLKYF
60 70 80 90 100
GAQSVRVLSD KGRLKHTAFA TFPNEKAAIK ALTRLHQLKL LGHTLVVEFA
110 120 130 140 150
KEQDRVHSPC PTSGSEKKKR SDDPVEDDKE KKELGYLTVE NGIAPNHGLT
160 170 180 190 200
FPLNSCLKYM YPPPSSTILA NIVNALASVP KFYVQVLHLM NKMNLPTPFG
210 220 230 240 250
PITARPPMYE DYMPLHAPLP PTSPQPPEEP PLPDEDEELS SEESEYESTD
260 270 280 290 300
DEDRQRMNKL MELANLQPKR PKTIKQRHVR KKRKIKDMLN TPLCPSHSSL
310 320 330 340 350
HPVLLPSDVF DQPQPVGNKR IEFHISTDMP AAFKKDLEKE QNCEEKNHDL
360 370 380 390 400
PATEVDASNI GFGKIFPKPN LDITEEIKED SDEMPSECIS RRELEKGRIS
410 420 430 440 450
REEMETLSVF RSYEPGEPNC RIYVKNLAKH VQEKDLKYIF GRYVDFSSET
460 470 480 490 500
QRIMFDIRLM KEGRMKGQAF IGLPNEKAAA KALKEANGYV LFGKPMVVQF
510
ARSARPKQDP KEGKRKC
Length:517
Mass (Da):58,575
Last modified:December 1, 2001 - v1
Checksum:iB71E12DB1E5BB736
GO
Isoform 2 (identifier: Q96LT9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     298-298: Missing.

Note: No experimental confirmation available.
Show »
Length:516
Mass (Da):58,488
Checksum:i7B819ED8377BD2B5
GO

Sequence cautioni

The sequence BAA90885 differs from that shown.Potential poly-A sequence.Curated
The sequence BAA90885 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAB47468 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti392 – 3921R → K in BAA90885 (PubMed:14702039).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei298 – 2981Missing in isoform 2. 2 PublicationsVSP_053413

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY099329 mRNA. Translation: AAM45139.1.
BK005195 mRNA. Translation: DAA05493.1.
AB058742 mRNA. Translation: BAB47468.1. Different initiation.
AK000015 mRNA. Translation: BAA90885.1. Sequence problems.
AK057799 mRNA. Translation: BAB71580.1.
AK289844 mRNA. Translation: BAF82533.1.
BX322653, AC095032, AC105272 Genomic DNA. Translation: CAH72167.1.
BX322653, AC095032 Genomic DNA. Translation: CAH72168.1.
CH471097 Genomic DNA. Translation: EAW72905.1.
CH471097 Genomic DNA. Translation: EAW72901.1.
CH471097 Genomic DNA. Translation: EAW72906.1.
BC010697 mRNA. Translation: AAH10697.2.
AL137730 mRNA. Translation: CAB70897.2.
CCDSiCCDS781.1. [Q96LT9-1]
PIRiT46396.
RefSeqiNP_060089.1. NM_017619.3. [Q96LT9-1]
UniGeneiHs.632423.

Genome annotation databases

EnsembliENST00000423855; ENSP00000391432; ENSG00000185946. [Q96LT9-1]
ENST00000524631; ENSP00000437278; ENSG00000185946. [Q96LT9-2]
ENST00000533099; ENSP00000432886; ENSG00000185946. [Q96LT9-1]
GeneIDi55599.
KEGGihsa:55599.
UCSCiuc010oum.2. human. [Q96LT9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY099329 mRNA. Translation: AAM45139.1.
BK005195 mRNA. Translation: DAA05493.1.
AB058742 mRNA. Translation: BAB47468.1. Different initiation.
AK000015 mRNA. Translation: BAA90885.1. Sequence problems.
AK057799 mRNA. Translation: BAB71580.1.
AK289844 mRNA. Translation: BAF82533.1.
BX322653, AC095032, AC105272 Genomic DNA. Translation: CAH72167.1.
BX322653, AC095032 Genomic DNA. Translation: CAH72168.1.
CH471097 Genomic DNA. Translation: EAW72905.1.
CH471097 Genomic DNA. Translation: EAW72901.1.
CH471097 Genomic DNA. Translation: EAW72906.1.
BC010697 mRNA. Translation: AAH10697.2.
AL137730 mRNA. Translation: CAB70897.2.
CCDSiCCDS781.1. [Q96LT9-1]
PIRiT46396.
RefSeqiNP_060089.1. NM_017619.3. [Q96LT9-1]
UniGeneiHs.632423.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EGNX-ray2.50A380-517[»]
ProteinModelPortaliQ96LT9.
SMRiQ96LT9. Positions 24-103, 387-506.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120740. 19 interactions.
IntActiQ96LT9. 6 interactions.
MINTiMINT-1180654.
STRINGi9606.ENSP00000391432.

PTM databases

iPTMnetiQ96LT9.
PhosphoSiteiQ96LT9.

Polymorphism and mutation databases

BioMutaiRNPC3.
DMDMi74760946.

Proteomic databases

EPDiQ96LT9.
MaxQBiQ96LT9.
PaxDbiQ96LT9.
PeptideAtlasiQ96LT9.
PRIDEiQ96LT9.

Protocols and materials databases

DNASUi55599.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000423855; ENSP00000391432; ENSG00000185946. [Q96LT9-1]
ENST00000524631; ENSP00000437278; ENSG00000185946. [Q96LT9-2]
ENST00000533099; ENSP00000432886; ENSG00000185946. [Q96LT9-1]
GeneIDi55599.
KEGGihsa:55599.
UCSCiuc010oum.2. human. [Q96LT9-1]

Organism-specific databases

CTDi55599.
GeneCardsiRNPC3.
HGNCiHGNC:18666. RNPC3.
HPAiHPA052434.
MalaCardsiRNPC3.
neXtProtiNX_Q96LT9.
Orphaneti231662. Isolated growth hormone deficiency type IA.
PharmGKBiPA134865246.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4206. Eukaryota.
ENOG410XQEY. LUCA.
GeneTreeiENSGT00530000063786.
HOGENOMiHOG000007217.
HOVERGENiHBG057088.
InParanoidiQ96LT9.
KOiK13157.
OMAiEDRQRMN.
OrthoDBiEOG091G0OCH.
PhylomeDBiQ96LT9.
TreeFamiTF324298.

Enzyme and pathway databases

ReactomeiR-HSA-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

ChiTaRSiRNPC3. human.
EvolutionaryTraceiQ96LT9.
GenomeRNAii55599.
PROiQ96LT9.

Gene expression databases

BgeeiENSG00000185946.
CleanExiHS_RNPC3.
ExpressionAtlasiQ96LT9. baseline and differential.
GenevisibleiQ96LT9. HS.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRBM40_HUMAN
AccessioniPrimary (citable) accession number: Q96LT9
Secondary accession number(s): A8K1C9
, D3DT74, Q5TZ87, Q96FK7, Q96JI8, Q9NSU7, Q9NXX2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: December 1, 2001
Last modified: September 7, 2016
This is version 143 of the entry and version 1 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 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.