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CASC3 CASC3 exon junction complex subunit [ Homo sapiens (human) ]

Gene ID: 22794, updated on 7-Apr-2024

Summary

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Official Symbol
CASC3provided by HGNC
Official Full Name
CASC3 exon junction complex subunitprovided by HGNC
Primary source
HGNC:HGNC:17040
See related
Ensembl:ENSG00000108349 MIM:606504; AllianceGenome:HGNC:17040
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BTZ; MLN51
Summary
The product of this gene is a core component of the exon junction complex (EJC), a protein complex that is deposited on spliced mRNAs at exon-exon junctions and functions in nonsense-mediated mRNA decay (NMD). The encoded protein binds RNA and interacts with two other EJC core components. It is predominantly located in the cytoplasm, but shuttles into the nucleus where it localizes to nuclear speckles. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 40.3), endometrium (RPKM 27.3) and 25 other tissues See more
Orthologs
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Genomic context

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See CASC3 in Genome Data Viewer
Location:
17q21.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (40140537..40172171)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (41004421..41036050)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38296790..38328424)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8480 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:38279065-38279703 Neighboring gene MSL complex subunit 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38296401-38297341 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38324317-38324876 Neighboring gene microRNA 6866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38332602-38333102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38333103-38333603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38333995-38334850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38334851-38335705 Neighboring gene Rap guanine nucleotide exchange factor like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38350695-38351195 Neighboring gene microRNA 6867 Neighboring gene Sharpr-MPRA regulatory region 10842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12134 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:38375397-38376175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38380779-38381350 Neighboring gene WAS/WASL interacting protein family member 2 Neighboring gene RNY4 pseudogene 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex. Gerbracht JV, et al. Nucleic Acids Res, 2020 Sep 4. PMID 32621609, Free PMC Article
  2. Metastatic lymph node 51 and fibroblast-like synoviocyte hyperproliferation in rheumatoid arthritis pathogenesis. Lim DS, et al. Rheumatol Int, 2011 Jul. PMID 21327427
  3. The exon-junction-complex-component metastatic lymph node 51 functions in stress-granule assembly. Baguet A, et al. J Cell Sci, 2007 Aug 15. PMID 17652158
  4. Mutational analysis of human eIF4AIII identifies regions necessary for exon junction complex formation and nonsense-mediated mRNA decay. Shibuya T, et al. RNA, 2006 Mar. PMID 16495234, Free PMC Article
  5. Targets of gene amplification and overexpression at 17q in gastric cancer. Varis A, et al. Cancer Res, 2002 May 1. PMID 11980659

See all (81) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex.
    Title: CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex.
  2. High CASC3 expression is associated with hepatocellular carcinoma.
    Title: Methylation-regulated miR-124-1 suppresses tumorigenesis in hepatocellular carcinoma by targeting CASC3.
  3. MLN51, alone or as part of the EJC, interacts directly with the pivotal eukaryotic translation initiation factor eIF3
    Title: EJC core component MLN51 interacts with eIF3 and activates translation.
  4. MLN51 is a key factor in fibroblast-like synoviocyte hyperplasia of rheumatoid arthritis patients.
    Title: Metastatic lymph node 51 and fibroblast-like synoviocyte hyperproliferation in rheumatoid arthritis pathogenesis.
  5. MLN51 is recruited into cytoplasmic aggregates known as stress granules (SGs) together with the SG-resident proteins.
    Title: The exon-junction-complex-component metastatic lymph node 51 functions in stress-granule assembly.
  6. data demonstrate that metastatic lymph node(MLN)51 protein associates with exon junction complex in the nucleus and remains stably associated with messenger RNA in the cytoplasm
    Title: Association of the breast cancer protein MLN51 with the exon junction complex via its speckle localizer and RNA binding module.
  7. crystal structure of a tetrameric exon junction core complex containing the DEAD-box adenosine triphosphatase eukaryotic initiation factor 4AIII bound to an ATP analog, MAGOH, Y14, a fragment of MLN51, and a polyuracil mRNA mimic
    Title: Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with cancer susceptibility candidate 3 (CASC3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

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 GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in intracellular mRNA localization IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA export from nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of translation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of U2-type catalytic step 1 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic stress granule IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
part_of exon-exon junction complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of exon-exon junction complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of exon-exon junction complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of exon-exon junction complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nuclear membrane IDA
Inferred from Direct Assay
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein CASC3
Names
MLN 51
barentsz
cancer susceptibility 3
cancer susceptibility candidate 3
cancer susceptibility candidate gene 3 protein
metastatic lymph node 51
metastatic lymph node gene 51 protein
protein barentsz

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_007359.5 → NP_031385.2  protein CASC3

    See identical proteins and their annotated locations for NP_031385.2

    Status: REVIEWED

    Source sequence(s)
    X80199
    Consensus CDS
    CCDS11362.1
    UniProtKB/Swiss-Prot
    A8K8R0, O15234
    UniProtKB/TrEMBL
    B4DKR6
    Related
    ENSP00000264645.6, ENST00000264645.12
    Conserved Domains (2) summary
    smart01044
    Location:146 → 248
    Btz; CASC3/Barentsz eIF4AIII binding
    PHA03247
    Location:555 → 703
    PHA03247; large tegument protein UL36; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    40140537..40172171
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435624.1 → XP_047291580.1  protein CASC3 isoform X3

  2. XM_005257163.3 → XP_005257220.1  protein CASC3 isoform X1

    See identical proteins and their annotated locations for XP_005257220.1

    UniProtKB/Swiss-Prot
    A8K8R0, O15234
    UniProtKB/TrEMBL
    B4DKR6
    Conserved Domains (2) summary
    smart01044
    Location:146 → 248
    Btz; CASC3/Barentsz eIF4AIII binding
    PHA03247
    Location:555 → 703
    PHA03247; large tegument protein UL36; Provisional

  3. XM_047435623.1 → XP_047291579.1  protein CASC3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    41004421..41036050
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054315482.1 → XP_054171457.1  protein CASC3 isoform X3

  2. XM_054315480.1 → XP_054171455.1  protein CASC3 isoform X1

    UniProtKB/Swiss-Prot
    A8K8R0, O15234

  3. XM_054315481.1 → XP_054171456.1  protein CASC3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15234.2 GenPept UniProtKB/Swiss-Prot:O15234

Gene LinkOut

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