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COL4A5 collagen type IV alpha 5 chain [ Homo sapiens (human) ]

Gene ID: 1287, updated on 7-Jun-2020

Summary

Official Symbol
COL4A5provided by HGNC
Official Full Name
collagen type IV alpha 5 chainprovided by HGNC
Primary source
HGNC:HGNC:2207
See related
Ensembl:ENSG00000188153 MIM:303630
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
ATS; ASLN; ATS1; CA54
Summary
This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Mutations in this gene are associated with X-linked Alport syndrome, also known as hereditary nephritis. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Aug 2010]
Expression
Broad expression in endometrium (RPKM 21.7), skin (RPKM 10.8) and 20 other tissues See more
Orthologs

Genomic context

See COL4A5 in Genome Data Viewer
Location:
Xq22.3
Exon count:
58
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (108439838..108697545)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (107683019..107940775)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene autophagy related 4A cysteine peptidase Neighboring gene collagen type IV alpha 6 chain Neighboring gene uncharacterized LOC101928358 Neighboring gene insulin receptor substrate 4 Neighboring gene RNA, U6 small nuclear 309, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Alport syndrome 1, X-linked recessive
MedGen: C4746986 OMIM: 301050 GeneReviews: Alport Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-03-22)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-03-22)

ClinGen Genome Curation Page

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 and serum-free macrophage supernatant (MSP) enhance synthesis of type IV collagen by mesangial cells; anti-TGF-beta antibodies attenuate this gp160/MSP-induced collagen synthesis PubMed
Tat tat Treatment with cannabinoids inhibits HIV-1 Tat-enhanced attachment of U937 cells to collagen IV, laminin, or ECM1 proteins, which is linked to the cannabinoid receptor type 2 and the modulation of beta1-integrin and actin distribution PubMed
tat HIV-1 Tat enhances adhesion of human U937 monocyte-like cells to proteins of the extracellular matrix, such as collagen IV, laminin, and ECM1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC42377, MGC167109, DKFZp686G1497

Gene Ontology Provided by GOA

Process Evidence Code Pubs
collagen-activated tyrosine kinase receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
neuromuscular junction development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
collagen-containing extracellular matrix HDA PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuromuscular junction IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
collagen alpha-5(IV) chain
Names
collagen IV, alpha-5 polypeptide
collagen of basement membrane, alpha-5 chain
collagen, type IV, alpha 5
dA149D17.3
dA24A23.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_011977.2 RefSeqGene

    Range
    4915..262622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000495.5NP_000486.1  collagen alpha-5(IV) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_000486.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame segment in the coding region, compared to variant 2. The resulting isoform (1) lacks two Gly-X-Y repeats, compared to isoform 2.
    Source sequence(s)
    AL034369, BC035387, BC151846, BU688037, DA461056, M31115
    Consensus CDS
    CCDS14543.1
    UniProtKB/Swiss-Prot
    P29400
    UniProtKB/TrEMBL
    A7MBN3, Q49AM6
    Related
    ENSP00000354505.2, ENST00000361603.7
    Conserved Domains (2) summary
    pfam01391
    Location:12851344
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:15731682
    C4; C-terminal tandem repeated domain in type 4 procollagen
  2. NM_033380.3NP_203699.1  collagen alpha-5(IV) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_203699.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longer isoform (2).
    Source sequence(s)
    AL034369, BC035387, BC151846, BU688037, DA461056, M31115
    Consensus CDS
    CCDS35366.1
    UniProtKB/Swiss-Prot
    P29400
    UniProtKB/TrEMBL
    A7MBN3, Q49AM6
    Related
    ENSP00000331902.6, ENST00000328300.10
    Conserved Domains (2) summary
    pfam01391
    Location:12911350
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:15791688
    C4; C-terminal tandem repeated domain in type 4 procollagen

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    108439838..108697545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530849.2XP_011529151.2  collagen alpha-5(IV) chain isoform X1

  2. XM_017029259.2XP_016884748.1  collagen alpha-5(IV) chain isoform X2

  3. XM_017029260.1XP_016884749.1  collagen alpha-5(IV) chain isoform X3

  4. XM_017029261.1XP_016884750.1  collagen alpha-5(IV) chain isoform X4

  5. XM_017029262.2XP_016884751.1  collagen alpha-5(IV) chain isoform X5

  6. XM_017029263.2XP_016884752.1  collagen alpha-5(IV) chain isoform X6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_033381.1: Suppressed sequence

    Description
    NM_033381.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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