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

Summary

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: mouse all
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Genomic context

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_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
High CASC3 expression is associated with hepatocellular carcinoma.
Title: Methylation-regulated miR-124-1 suppresses tumorigenesis in hepatocellular carcinoma by targeting CASC3.
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.
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.
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.
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.
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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G19968 (e-PCR)
- UniSTS:10250

A002D45 (e-PCR)
- UniSTS:10251

SGC31792 (e-PCR)
- UniSTS:23895

D17S1417E (e-PCR)
- UniSTS:150461

D17S1436E (e-PCR)
- UniSTS:150474

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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)

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

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

40140537..40172171

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047435624.1 → XP_047291580.1 protein CASC3 isoform X3
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
XM_047435623.1 → XP_047291579.1 protein CASC3 isoform X2