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

Gene ID: 1286, updated on 26-Aug-2014
Official Symbol
COL4A4provided by HGNC
Official Full Name
collagen, type IV, alpha 4provided by HGNC
Primary source
HGNC:2206
See related
Ensembl:ENSG00000081052; HPRD:00360; MIM:120131; Vega:OTTHUMG00000149892
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
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]
See COL4A4 in Epigenomics, MapViewer
Location:
2q35-q37
Exon count:
57
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 2 NC_000002.12 (226968916..227164559, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (227867427..228029275, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene microRNA 5702 Neighboring gene insulin receptor substrate 1 Neighboring gene rhomboid domain containing 1 Neighboring gene uncharacterized LOC102723537 Neighboring gene collagen, type IV, alpha 3 (Goodpasture antigen) Neighboring gene uncharacterized LOC654841 Neighboring gene stress-induced phosphoprotein 1 pseudogene 2 Neighboring gene mitochondrial fission factor

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

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

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

Go to the HIV-1, Human Protein Interaction Database

  • Amoebiasis, organism-specific biosystem (from KEGG)
    Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • Amoebiasis, conserved biosystem (from KEGG)
    Amoebiasis, conserved biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
    Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
    Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • ECM-receptor interaction, organism-specific biosystem (from KEGG)
    ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • ECM-receptor interaction, conserved biosystem (from KEGG)
    ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Focal Adhesion, organism-specific biosystem (from WikiPathways)
    Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, organism-specific biosystem (from KEGG)
    Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, conserved biosystem (from KEGG)
    Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
    Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...
  • NCAM signaling for neurite out-growth, organism-specific biosystem (from REACTOME)
    NCAM signaling for neurite out-growth, organism-specific biosystemThe neural cell adhesion molecule, NCAM, is a member of the immunoglobulin (Ig) superfamily and is involved in a variety of cellular processes of importance for the formation and maintenance of the n...
  • NCAM1 interactions, organism-specific biosystem (from REACTOME)
    NCAM1 interactions, organism-specific biosystemThe neural cell adhesion molecule, NCAM1 is generally considered as a cell adhesion mediator, but it is also considered to be a signal transducing receptor molecule. NCAM1 is involved in multiple cis...
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
    PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • Pathways in cancer, organism-specific biosystem (from KEGG)
    Pathways in cancer, organism-specific biosystem
    Pathways in cancer
  • Protein digestion and absorption, organism-specific biosystem (from KEGG)
    Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Protein digestion and absorption, conserved biosystem (from KEGG)
    Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by PDGF, organism-specific biosystem (from REACTOME)
    Signaling by PDGF, organism-specific biosystemPlatelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary end...
  • Small cell lung cancer, organism-specific biosystem (from KEGG)
    Small cell lung cancer, organism-specific biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...
  • Small cell lung cancer, conserved biosystem (from KEGG)
    Small cell lung cancer, conserved biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
axon guidance TAS
Traceable Author Statement
more info
 
collagen catabolic process TAS
Traceable Author Statement
more info
 
extracellular matrix disassembly TAS
Traceable Author Statement
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
glomerular basement membrane development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
basal lamina IDA
Inferred from Direct Assay
more info
PubMed 
collagen type IV trimer IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
Preferred Names
collagen alpha-4(IV) chain
Names
collagen alpha-4(IV) chain
Collagen IV, alpha-4 polypeptide
collagen of basement membrane, alpha-4 chain

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 

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

mRNA and Protein(s)

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

    See proteins identical to NP_000083.3

    Status: REVIEWED

    Source sequence(s)
    AC073149, AC079235, BX094848, X81053
    Consensus CDS
    CCDS42828.1
    UniProtKB/Swiss-Prot
    P53420
    Related
    ENSP00000379866, OTTHUMP00000195046, ENST00000396625, OTTHUMT00000313770
    Conserved Domains (2) summary
    pfam01413
    Location:14651572
    Blast Score: 501
    C4; C-terminal tandem repeated domain in type 4 procollagen
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000002.12 

    Range
    226968916..227164559
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006712249.1XP_006712312.1  

    Conserved Domains (3) summary
    pfam01413
    Location:14651572
    Blast Score: 502
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:15731609
    Blast Score: 174
    C4; C-terminal tandem repeated domain in type 4 procollagen
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)
  2. XM_006712250.1XP_006712313.1  

    Conserved Domains (3) summary
    pfam01413
    Location:14651572
    Blast Score: 502
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:15731606
    Blast Score: 171
    C4; C-terminal tandem repeated domain in type 4 procollagen
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)
  3. XM_006712247.1XP_006712310.1  

    See proteins identical to XP_006712310.1

    Conserved Domains (3) summary
    pfam01413
    Location:14651572
    Blast Score: 503
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:15731605
    Blast Score: 170
    C4; C-terminal tandem repeated domain in type 4 procollagen
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)
  4. XM_006712252.1XP_006712315.1  

    Conserved Domains (1) summary
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)
  5. XM_006712248.1XP_006712311.1  

    See proteins identical to XP_006712311.1

    Conserved Domains (3) summary
    pfam01413
    Location:14651572
    Blast Score: 503
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:15731605
    Blast Score: 170
    C4; C-terminal tandem repeated domain in type 4 procollagen
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)
  6. XM_005246281.1XP_005246338.1  

    See proteins identical to XP_005246338.1

    UniProtKB/Swiss-Prot
    P53420
    Conserved Domains (2) summary
    pfam01413
    Location:14651572
    Blast Score: 501
    C4; C-terminal tandem repeated domain in type 4 procollagen
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)
  7. XM_005246282.1XP_005246339.1  

    Conserved Domains (2) summary
    pfam01413
    Location:12801387
    Blast Score: 501
    C4; C-terminal tandem repeated domain in type 4 procollagen
    pfam01391
    Location:644695
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)
  8. XM_006712246.1XP_006712309.1  

    Conserved Domains (3) summary
    pfam01413
    Location:15101625
    Blast Score: 430
    C4; C-terminal tandem repeated domain in type 4 procollagen
    cl02467
    Location:14361509
    Blast Score: 305
    C4; C-terminal tandem repeated domain in type 4 procollagen
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)
  9. XM_006712251.1XP_006712314.1  

    Conserved Domains (1) summary
    pfam01391
    Location:829880
    Blast Score: 108
    Collagen; Collagen triple helix repeat (20 copies)

RNA

  1. XR_427068.1 RNA Sequence

  2. XR_427065.1 RNA Sequence

  3. XR_427067.1 RNA Sequence

  4. XR_427066.1 RNA Sequence

Alternate HuRef

Genomic

  1. AC_000134.1 

    Range
    219710854..219872782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 

    Range
    227873296..228035468
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)