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Rnpc3 RNA-binding region (RNP1, RRM) containing 3 [ Mus musculus (house mouse) ]

Gene ID: 67225, updated on 21-Apr-2024

Summary

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Official Symbol
Rnpc3provided by MGI
Official Full Name
RNA-binding region (RNP1, RRM) containing 3provided by MGI
Primary source
MGI:MGI:1914475
See related
Ensembl:ENSMUSG00000027981 AllianceGenome:MGI:1914475
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
2810441O16Rik; C030014B17Rik
Summary
Predicted to enable U12 snRNA binding activity and pre-mRNA intronic binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be part of U12-type spliceosomal complex. Is expressed in central nervous system; dorsal root ganglion; nose; and trigeminal nerve. Human ortholog(s) of this gene implicated in isolated growth hormone deficiency. Orthologous to human RNPC3 (RNA binding region (RNP1, RRM) containing 3). [provided by Alliance of Genome Resources, Apr 2022]
Annotation information
Annotation category: suggests misassembly
Expression
Broad expression in CNS E18 (RPKM 16.8), CNS E14 (RPKM 13.4) and 24 other tissues See more
Orthologs
human all
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Genomic context

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Location:
3 F3; 3 49.35 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (113398716..113423798, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (113605067..113630149, complement)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene amylase 2a1 Neighboring gene amylase 1, salivary Neighboring gene STARR-positive B cell enhancer mm9_chr3:113308015-113308316 Neighboring gene STARR-positive B cell enhancer mm9_chr3:113332370-113332671 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:113332840-113333141 Neighboring gene ribosomal protein L5 pseudogene Neighboring gene STARR-seq mESC enhancer starr_08733 Neighboring gene mortality factor 4 like 2 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Early developmental arrest and impaired gastrointestinal homeostasis in U12-dependent splicing-defective Rnpc3-deficient mice. Doggett K, et al. RNA, 2018 Dec. PMID 30254136, Free PMC Article
  2. Srsf10 and the minor spliceosome control tissue-specific and dynamic SR protein expression. Meinke S, et al. Elife, 2020 Apr 27. PMID 32338600, Free PMC Article
  3. Minor spliceosome components are predominantly localized in the nucleus. Pessa HK, et al. Proc Natl Acad Sci U S A, 2008 Jun 24. PMID 18559850, Free PMC Article
  4. PRC1 and PRC2 are not required for targeting of H2A.Z to developmental genes in embryonic stem cells. Illingworth RS, et al. PLoS One, 2012. PMID 22496869, Free PMC Article
  5. Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways. Thiagarajan RD, et al. PLoS One, 2011 Feb 28. PMID 21386911, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (3) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables U12 snRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables pre-mRNA intronic binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U12-type spliceosomal complex ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
RNA-binding region-containing protein 3
Names
RNA-binding motif protein 40
RNA-binding protein 40

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001038696.1 → NP_001033785.1  RNA-binding region-containing protein 3 isoform a

    See identical proteins and their annotated locations for NP_001033785.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 encode the same protein (isoform a).
    Source sequence(s)
    AK134241, AK161063, BY004661
    Consensus CDS
    CCDS17777.1
    UniProtKB/Swiss-Prot
    Q3TTZ2, Q3UZ01, Q69Z94, Q80VS9, Q91YJ1, Q9CSC1
    UniProtKB/TrEMBL
    F6TN13
    Related
    ENSMUSP00000089792.4, ENSMUST00000092154.10
    Conserved Domains (3) summary
    COG0724
    Location:311 → 509
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12238
    Location:28 → 100
    RRM1_RBM40_like; RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins
    cd12239
    Location:417 → 499
    RRM2_RBM40_like; RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

  2. NM_001287015.1 → NP_001273944.1  RNA-binding region-containing protein 3 isoform b

    See identical proteins and their annotated locations for NP_001273944.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. It encodes isoform b which is shorter than isoform a.
    Source sequence(s)
    AK134241, AK161063, BY004586
    Consensus CDS
    CCDS71308.1
    UniProtKB/TrEMBL
    F6TN13
    Related
    ENSMUSP00000102145.2, ENSMUST00000106535.2
    Conserved Domains (3) summary
    COG0724
    Location:311 → 513
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12238
    Location:28 → 100
    RRM1_RBM40_like; RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins
    cd12239
    Location:417 → 496
    RRM2_RBM40_like; RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

  3. NM_026043.3 → NP_080319.2  RNA-binding region-containing protein 3 isoform a

    See identical proteins and their annotated locations for NP_080319.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 encode the same protein (isoform a).
    Source sequence(s)
    AK134241, BC043695, BY004661
    Consensus CDS
    CCDS17777.1
    UniProtKB/Swiss-Prot
    Q3TTZ2, Q3UZ01, Q69Z94, Q80VS9, Q91YJ1, Q9CSC1
    UniProtKB/TrEMBL
    F6TN13
    Related
    ENSMUSP00000102146.2, ENSMUST00000106536.8
    Conserved Domains (3) summary
    COG0724
    Location:311 → 509
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12238
    Location:28 → 100
    RRM1_RBM40_like; RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins
    cd12239
    Location:417 → 499
    RRM2_RBM40_like; RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    113398716..113423798 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3UZ01.2 GenPept UniProtKB/Swiss-Prot:Q3UZ01

Gene LinkOut

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