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COL4A4 collagen type IV alpha 4 chain [ Homo sapiens (human) ]

Gene ID: 1286, updated on 5-Aug-2022

Summary

Official Symbol
COL4A4provided by HGNC
Official Full Name
collagen type IV alpha 4 chainprovided by HGNC
Primary source
HGNC:HGNC:2206
See related
Ensembl:ENSG00000081052 MIM:120131; AllianceGenome:HGNC:2206
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
BFH; ATS2; CA44
Summary
This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. This particular collagen IV subunit, however, is only found in a subset of basement membranes. 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. Mutations in this gene are associated with type II autosomal recessive Alport syndrome (hereditary glomerulonephropathy) and with familial benign hematuria (thin basement membrane disease). Two transcripts, differing only in their transcription start sites, have been identified for this gene and, as is common for collagen genes, multiple polyadenylation sites are found in the 3' UTR. [provided by RefSeq, Jul 2008]
Expression
Broad expression in kidney (RPKM 5.3), thyroid (RPKM 4.9) and 18 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See COL4A4 in Genome Data Viewer
Location:
2q36.3
Exon count:
57
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (226967360..227164488, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (227485408..227646963, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (227867430..228028921, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 11623 Neighboring gene insulin receptor substrate 1 Neighboring gene Sharpr-MPRA regulatory region 3963 Neighboring gene rhomboid domain containing 1 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene collagen type IV alpha 3 chain Neighboring gene MFF divergent transcript Neighboring gene stress induced phosphoprotein 1 pseudogene 2 Neighboring gene mitochondrial fission factor

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
MedGen: C1567741 GeneReviews: Not available
Compare labs
Autosomal recessive Alport syndrome
MedGen: C4746745 OMIM: 203780 GeneReviews: Alport Syndrome
Compare labs
Benign familial hematuria
MedGen: C0241908 OMIM: 141200 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
EBI GWAS Catalog

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 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
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

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in glomerular basement membrane development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in glomerular basement membrane development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in basement membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in basement membrane IDA
Inferred from Direct Assay
more info
PubMed 
part_of collagen type IV trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of collagen type IV trimer IDA
Inferred from Direct Assay
more info
PubMed 
located_in collagen-containing extracellular matrix HDA PubMed 
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-4(IV) chain
Names
Collagen IV, alpha-4 polypeptide
collagen of basement membrane, alpha-4 chain
collagen, type IV, alpha 4

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_011592.1 RefSeqGene

    Range
    5001..166849
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_231

mRNA and Protein(s)

  1. NM_000092.5NP_000083.3  collagen alpha-4(IV) chain precursor

    See identical proteins and their annotated locations for NP_000083.3

    Status: REVIEWED

    Source sequence(s)
    AC073149, AC079235, BX094848, X81053
    Consensus CDS
    CCDS42828.1
    UniProtKB/Swiss-Prot
    P53420, Q53WR1
    Related
    ENSP00000379866.3, ENST00000396625.5
    Conserved Domains (2) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14661570
    C4; C-terminal tandem repeated domain in type 4 procollagen

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    226967360..227164488 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510565.3XP_011508867.1  collagen alpha-4(IV) chain isoform X10

    Conserved Domains (1) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
  2. XM_011510570.3XP_011508872.1  collagen alpha-4(IV) chain isoform X13

    See identical proteins and their annotated locations for XP_011508872.1

    Conserved Domains (1) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
  3. XM_011510562.3XP_011508864.1  collagen alpha-4(IV) chain isoform X7

    See identical proteins and their annotated locations for XP_011508864.1

    Conserved Domains (3) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14661570
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:15741607
    C4; C-terminal tandem repeated domain in type 4 procollagen
  4. XM_047443250.1XP_047299206.1  collagen alpha-4(IV) chain isoform X13

  5. XM_047443245.1XP_047299201.1  collagen alpha-4(IV) chain isoform X7

  6. XM_011510569.3XP_011508871.1  collagen alpha-4(IV) chain isoform X13

    See identical proteins and their annotated locations for XP_011508871.1

    Conserved Domains (1) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
  7. XM_011510567.3XP_011508869.1  collagen alpha-4(IV) chain isoform X11

    See identical proteins and their annotated locations for XP_011508869.1

    Conserved Domains (1) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
  8. XM_047443249.1XP_047299205.1  collagen alpha-4(IV) chain isoform X11

  9. XM_011510566.3XP_011508868.1  collagen alpha-4(IV) chain isoform X11

    See identical proteins and their annotated locations for XP_011508868.1

    Conserved Domains (1) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
  10. XM_047443248.1XP_047299204.1  collagen alpha-4(IV) chain isoform X11

  11. XM_011510561.3XP_011508863.1  collagen alpha-4(IV) chain isoform X7

    See identical proteins and their annotated locations for XP_011508863.1

    Conserved Domains (3) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14661570
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:15741607
    C4; C-terminal tandem repeated domain in type 4 procollagen
  12. XM_011510560.3XP_011508862.1  collagen alpha-4(IV) chain isoform X6

    See identical proteins and their annotated locations for XP_011508862.1

    Conserved Domains (3) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14661570
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:15741605
    C4; C-terminal tandem repeated domain in type 4 procollagen
  13. XM_047443242.1XP_047299198.1  collagen alpha-4(IV) chain isoform X6

  14. XM_011510559.3XP_011508861.1  collagen alpha-4(IV) chain isoform X6

    See identical proteins and their annotated locations for XP_011508861.1

    Conserved Domains (3) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14661570
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:15741605
    C4; C-terminal tandem repeated domain in type 4 procollagen
  15. XM_047443241.1XP_047299197.1  collagen alpha-4(IV) chain isoform X6

  16. XM_047443228.1XP_047299184.1  collagen alpha-4(IV) chain isoform X1

    UniProtKB/Swiss-Prot
    Q53WR1
  17. XM_005246281.4XP_005246338.1  collagen alpha-4(IV) chain isoform X1

    See identical proteins and their annotated locations for XP_005246338.1

    UniProtKB/Swiss-Prot
    P53420, Q53WR1
    Conserved Domains (2) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14661570
    C4; C-terminal tandem repeated domain in type 4 procollagen
  18. XM_005246282.4XP_005246339.1  collagen alpha-4(IV) chain isoform X8

    Conserved Domains (2) summary
    pfam01391
    Location:644695
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:12811385
    C4; C-terminal tandem repeated domain in type 4 procollagen
  19. XM_011510558.3XP_011508860.1  collagen alpha-4(IV) chain isoform X3

    Conserved Domains (2) summary
    pfam01391
    Location:793844
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14301534
    C4; C-terminal tandem repeated domain in type 4 procollagen
  20. XM_011510557.3XP_011508859.1  collagen alpha-4(IV) chain isoform X2

    Conserved Domains (2) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14391543
    C4; C-terminal tandem repeated domain in type 4 procollagen
  21. XM_017003297.2XP_016858786.1  collagen alpha-4(IV) chain isoform X4

  22. XM_006712246.4XP_006712309.1  collagen alpha-4(IV) chain isoform X5

    Conserved Domains (3) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:15111623
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:14451507
    C4; C-terminal tandem repeated domain in type 4 procollagen
  23. XM_011510572.4XP_011508874.1  collagen alpha-4(IV) chain isoform X14

    Conserved Domains (2) summary
    pfam01391
    Location:271322
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:9081012
    C4; C-terminal tandem repeated domain in type 4 procollagen
  24. XM_047443246.1XP_047299202.1  collagen alpha-4(IV) chain isoform X9

  25. XM_011510568.3XP_011508870.1  collagen alpha-4(IV) chain isoform X12

    Conserved Domains (1) summary
    pfam01391
    Location:829880
    Collagen; Collagen triple helix repeat (20 copies)

RNA

  1. XR_922837.3 RNA Sequence

  2. XR_001738602.2 RNA Sequence

  3. XR_007069255.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    227485408..227646963 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)