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Protein

RNA-binding protein 40

Gene

Rnpc3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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 (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-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
Gene namesi
Name:Rnpc3
Synonyms:Kiaa1839, Rbm40
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:1914475. Rnpc3.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 514514RNA-binding protein 40PRO_0000311113Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei21 – 211PhosphoserineBy similarity
Modified residuei108 – 1081PhosphoserineBy similarity
Modified residuei349 – 3491PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ3UZ01.
MaxQBiQ3UZ01.
PaxDbiQ3UZ01.
PRIDEiQ3UZ01.

PTM databases

iPTMnetiQ3UZ01.
PhosphoSiteiQ3UZ01.

Expressioni

Gene expression databases

BgeeiQ3UZ01.
CleanExiMM_RNPC3.
ExpressionAtlasiQ3UZ01. baseline and differential.
GenevisibleiQ3UZ01. MM.

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 (By similarity).By similarity

Protein-protein interaction databases

BioGridi212030. 1 interaction.
STRINGi10090.ENSMUSP00000089792.

Structurei

3D structure databases

ProteinModelPortaliQ3UZ01.
SMRiQ3UZ01. Positions 387-504.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini27 – 10276RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini418 – 50184RRM 2PROSITE-ProRule annotationAdd
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.
InParanoidiQ3UZ01.
KOiK13157.
OMAiEDRQRMN.
PhylomeDBiQ3UZ01.
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: Q3UZ01-1) [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
MAGPEPPMPL SRGGPGSASL SPPRGDRTLL VRHLPAELTA EEKEDLLKYF
60 70 80 90 100
GAQSVRVLSD KGRLKHTAFA TFPNEKAAIK ALTRLHQLKL LGHTLVVEFA
110 120 130 140 150
KEQDRVHSPC STSNTEKKKR LDDTVENDKE KKEPDILTVE NGIAPNHGLT
160 170 180 190 200
FPLNSCLKYM YPPPSSTILA NIVNALASVP KFYVQVLHLM NKMNLPTPFG
210 220 230 240 250
PITARPPMYE DYMPLHAPLP PTSPQPPEEP PLPDEDEDLS SKESEYESSD
260 270 280 290 300
EEDRQRMNRL MELANLQPKR PKTEKPRHVR KKRKIKDMLN IPSSASHSLH
310 320 330 340 350
PVLLPSDVFD QPQSVGNKKI EFNISTNMPA AFNKDLETQP NNEEENSDSP
360 370 380 390 400
DTGLDSNTGF GKIFPKPNLN ITEEITEDSD EIPSQFISRK ELEKGRISRE
410 420 430 440 450
EMETLSVFRS YEPGEPNCRI YVKNLARHVQ EKDLKFIFGR YVDFSSETQR
460 470 480 490 500
IMFDIRLMKE GRMKGQAFVG LPNEKAAAKA LKEANGYVLF GKPMVVQFAR
510
SARPKQDSKE GKRK
Length:514
Mass (Da):57,972
Last modified:November 13, 2007 - v2
Checksum:i0FB772119ED29A0D
GO
Isoform 2 (identifier: Q3UZ01-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     497-497: Missing.

Show »
Length:513
Mass (Da):57,844
Checksum:i155DCF403377C0D5
GO

Sequence cautioni

The sequence AAH16603.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti41 – 411E → K in BAE22060 (PubMed:16141072).Curated
Sequence conflicti261 – 2611M → T in BAB28770 (PubMed:16141072).Curated
Sequence conflicti422 – 4221V → E in BAE22060 (PubMed:16141072).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei497 – 4971Missing in isoform 2. 1 PublicationVSP_029402

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK013288 mRNA. Translation: BAB28770.3.
AK134241 mRNA. Translation: BAE22060.1.
AK161063 mRNA. Translation: BAE36180.1.
BC016603 mRNA. Translation: AAH16603.1. Different initiation.
BC043695 mRNA. Translation: AAH43695.1.
AK173272 mRNA. Translation: BAD32550.1.
CCDSiCCDS17777.1. [Q3UZ01-1]
CCDS71308.1. [Q3UZ01-2]
RefSeqiNP_001033785.1. NM_001038696.1. [Q3UZ01-1]
NP_001273944.1. NM_001287015.1. [Q3UZ01-2]
NP_080319.2. NM_026043.3. [Q3UZ01-1]
UniGeneiMm.316928.

Genome annotation databases

EnsembliENSMUST00000092154; ENSMUSP00000089792; ENSMUSG00000027981. [Q3UZ01-1]
ENSMUST00000106535; ENSMUSP00000102145; ENSMUSG00000027981. [Q3UZ01-2]
ENSMUST00000106536; ENSMUSP00000102146; ENSMUSG00000027981. [Q3UZ01-1]
GeneIDi67225.
KEGGimmu:67225.
UCSCiuc008rbd.1. mouse. [Q3UZ01-1]
uc008rbf.1. mouse. [Q3UZ01-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK013288 mRNA. Translation: BAB28770.3.
AK134241 mRNA. Translation: BAE22060.1.
AK161063 mRNA. Translation: BAE36180.1.
BC016603 mRNA. Translation: AAH16603.1. Different initiation.
BC043695 mRNA. Translation: AAH43695.1.
AK173272 mRNA. Translation: BAD32550.1.
CCDSiCCDS17777.1. [Q3UZ01-1]
CCDS71308.1. [Q3UZ01-2]
RefSeqiNP_001033785.1. NM_001038696.1. [Q3UZ01-1]
NP_001273944.1. NM_001287015.1. [Q3UZ01-2]
NP_080319.2. NM_026043.3. [Q3UZ01-1]
UniGeneiMm.316928.

3D structure databases

ProteinModelPortaliQ3UZ01.
SMRiQ3UZ01. Positions 387-504.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi212030. 1 interaction.
STRINGi10090.ENSMUSP00000089792.

PTM databases

iPTMnetiQ3UZ01.
PhosphoSiteiQ3UZ01.

Proteomic databases

EPDiQ3UZ01.
MaxQBiQ3UZ01.
PaxDbiQ3UZ01.
PRIDEiQ3UZ01.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000092154; ENSMUSP00000089792; ENSMUSG00000027981. [Q3UZ01-1]
ENSMUST00000106535; ENSMUSP00000102145; ENSMUSG00000027981. [Q3UZ01-2]
ENSMUST00000106536; ENSMUSP00000102146; ENSMUSG00000027981. [Q3UZ01-1]
GeneIDi67225.
KEGGimmu:67225.
UCSCiuc008rbd.1. mouse. [Q3UZ01-1]
uc008rbf.1. mouse. [Q3UZ01-2]

Organism-specific databases

CTDi55599.
MGIiMGI:1914475. Rnpc3.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG4206. Eukaryota.
ENOG410XQEY. LUCA.
GeneTreeiENSGT00530000063786.
HOGENOMiHOG000007217.
HOVERGENiHBG057088.
InParanoidiQ3UZ01.
KOiK13157.
OMAiEDRQRMN.
PhylomeDBiQ3UZ01.
TreeFamiTF324298.

Enzyme and pathway databases

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

Miscellaneous databases

PROiQ3UZ01.
SOURCEiSearch...

Gene expression databases

BgeeiQ3UZ01.
CleanExiMM_RNPC3.
ExpressionAtlasiQ3UZ01. baseline and differential.
GenevisibleiQ3UZ01. MM.

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...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J.
    Tissue: Embryo, Skin and Thymus.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: Czech II and FVB/N.
    Tissue: Mammary tumor.
  3. "Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
    Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., Saga Y., Seino S., Nishimura M., Kaisho T., Hoshino K., Kitamura H., Nagase T., Ohara O., Koga H.
    DNA Res. 11:205-218(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 53-514 (ISOFORM 1).
    Tissue: Fetal brain.

Entry informationi

Entry nameiRBM40_MOUSE
AccessioniPrimary (citable) accession number: Q3UZ01
Secondary accession number(s): Q3TTZ2
, Q69Z94, Q80VS9, Q91YJ1, Q9CSC1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: November 13, 2007
Last modified: July 6, 2016
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.