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CNIH4 cornichon family member 4 [ Homo sapiens (human) ]

Gene ID: 29097, updated on 5-Mar-2024

Summary

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Official Symbol
CNIH4provided by HGNC
Official Full Name
cornichon family member 4provided by HGNC
Primary source
HGNC:HGNC:25013
See related
Ensembl:ENSG00000143771 MIM:617483; AllianceGenome:HGNC:25013
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CNIH2; CNIH-4; HSPC163
Summary
Enables CCR5 chemokine receptor binding activity. Involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Located in endoplasmic reticulum and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in placenta (RPKM 7.6), colon (RPKM 7.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q42.11
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (224356803..224379452)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (223545746..223568267)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (224544581..224567154)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nuclear VCP like Neighboring gene RNA, U6 small nuclear 1008, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2608 Neighboring gene Sharpr-MPRA regulatory region 12366 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:224523487-224523975 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:224527150-224527870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224528593-224529312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2609 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224544931-224545431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224616083-224616672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224616673-224617262 Neighboring gene WD repeat domain 26 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1853 Neighboring gene microRNA 4742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2612 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:224661692-224661861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224667779-224668305 Neighboring gene cornichon family AMPA receptor auxiliary protein 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:224685507-224686036 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224686037-224686568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:224687944-224688444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:224688445-224688945 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224696756-224697667 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:224703315-224703519 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224759465-224759964 Neighboring gene aldehyde reductase family 1 member B1 pseudogene 1

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. Potential roles of Cornichon Family AMPA Receptor Auxiliary Protein 4 (CNIH4) in head and neck squamous cell carcinoma. Liu H, et al. Cancer Biomark, 2022. PMID 36404537
  2. Screening and identification of CNIH4 gene associated with cell proliferation in gastric cancer based on a large-scale CRISPR-Cas9 screening database DepMap. Zhang H, et al. Gene, 2023 Jan 20. PMID 36220450
  3. Using circular RNA hsa_circ_0000190 as a new biomarker in the diagnosis of gastric cancer. Chen S, et al. Clin Chim Acta, 2017 Mar. PMID 28130019
  4. CNIH4 interacts with newly synthesized GPCR and controls their export from the endoplasmic reticulum. Sauvageau E, et al. Traffic, 2014 Apr. PMID 24405750
  5. Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned. Wray NR, et al. Mol Psychiatry, 2012 Jan. PMID 21042317, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Comprehensive analysis of clinical prognosis and biological significance of CNIH4 in cervical cancer.
    Title: Comprehensive analysis of clinical prognosis and biological significance of CNIH4 in cervical cancer.
  2. Potential roles of Cornichon Family AMPA Receptor Auxiliary Protein 4 (CNIH4) in head and neck squamous cell carcinoma.
    Title: Potential roles of Cornichon Family AMPA Receptor Auxiliary Protein 4 (CNIH4) in head and neck squamous cell carcinoma.
  3. Screening and identification of CNIH4 gene associated with cell proliferation in gastric cancer based on a large-scale CRISPR-Cas9 screening database DepMap.
    Title: Screening and identification of CNIH4 gene associated with cell proliferation in gastric cancer based on a large-scale CRISPR-Cas9 screening database DepMap.
  4. hsa_circ_0000190 (gene symbol is CNIH4) may be a novel non-invasive biomarker for the diagnosis of gastric cancer
    Title: Using circular RNA hsa_circ_0000190 as a new biomarker in the diagnosis of gastric cancer.
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

EBI GWAS Catalog

Description
Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned.
EBI GWAS Catalog

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

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 CCR5 chemokine receptor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in COPII-coated ER to Golgi transport vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum-Golgi intermediate compartment IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
protein cornichon homolog 4
Names
cornichon family AMPA receptor auxiliary protein 4
cornichon homolog 4

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_001277197.2 → NP_001264126.1  protein cornichon homolog 4 isoform 2

    See identical proteins and their annotated locations for NP_001264126.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC099790, AK289973, BC039037
    Consensus CDS
    CCDS60430.1
    UniProtKB/TrEMBL
    A6NJ96
    Related
    ENSP00000355822.5, ENST00000366857.9
    Conserved Domains (1) summary
    pfam03311
    Location:3 → 86
    Cornichon; Cornichon protein

  2. NM_001277198.2 → NP_001264127.1  protein cornichon homolog 4 isoform 3

    See identical proteins and their annotated locations for NP_001264127.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' splice junction in a 3' exon compared to variant 1, that causes a frameshift. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC099790, BC039037, BI752106, DA185135
    Conserved Domains (1) summary
    pfam03311
    Location:3 → 84
    Cornichon; Cornichon protein

  3. NM_001277199.2 → NP_001264128.1  protein cornichon homolog 4 isoform 4

    See identical proteins and their annotated locations for NP_001264128.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon and contains an alternate exon compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC099790, BC039037, BQ051754, DA185135
    Conserved Domains (1) summary
    pfam03311
    Location:1 → 67
    Cornichon; Cornichon protein

  4. NM_001277200.2 → NP_001264129.1  protein cornichon homolog 4 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate downstream exon in place of the last exon of variant 1. The resulting isoform (5) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BQ575976, DA185135, HY145928
    Consensus CDS
    CCDS60429.1
    UniProtKB/TrEMBL
    A6NLH6, Q53HE6
    Related
    ENSP00000355821.3, ENST00000366856.3
    Conserved Domains (1) summary
    pfam03311
    Location:3 → 130
    Cornichon; Cornichon protein

  5. NM_014184.4 → NP_054903.1  protein cornichon homolog 4 isoform 1

    See identical proteins and their annotated locations for NP_054903.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC099790, BC000573, BC039037, DA185135
    Consensus CDS
    CCDS1543.1
    UniProtKB/Swiss-Prot
    A8K1Q8, B2R553, Q9H0X8, Q9P003
    UniProtKB/TrEMBL
    Q53HE6
    Related
    ENSP00000420443.1, ENST00000465271.6
    Conserved Domains (1) summary
    pfam03311
    Location:3 → 130
    Cornichon; Cornichon protein

RNA

  1. NR_102347.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate splice junction at the 3' end of the first exon and lacks an alternate exon compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC099790, BC039037, DA185135, HY018269

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    224356803..224379452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418620.1 → XP_047274576.1  protein cornichon homolog 4 isoform X1

  2. XM_047418623.1 → XP_047274579.1  protein cornichon homolog 4 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    223545746..223568267
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P003.1 GenPept UniProtKB/Swiss-Prot:Q9P003

Gene LinkOut

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