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

    Gene ID: 1286, updated on 19-Mar-2019

    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
    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

    Genomic context

    See COL4A4 in Genome Data Viewer
    Location:
    2q36.3
    Exon count:
    54
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (226970293..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 collagen type IV alpha 3 chain Neighboring gene uncharacterized LOC654841 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 FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Alport syndrome, autosomal recessive
    MedGen: C1567744 OMIM: 203780 GeneReviews: Alport Syndrome
    Compare labs
    Benign familial hematuria
    MedGen: C0241908 OMIM: 141200 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

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

    • AGE-RAGE signaling pathway in diabetic complications, organism-specific biosystem (from KEGG)
      AGE-RAGE signaling pathway in diabetic complications, organism-specific biosystemAdvanced glycation end products (AGEs) are a complex group of compounds produced through the non-enzymatic glycation and oxidation of proteins, lipids and nucleic acids, primarily due to aging and un...
    • AGE-RAGE signaling pathway in diabetic complications, conserved biosystem (from KEGG)
      AGE-RAGE signaling pathway in diabetic complications, conserved biosystemAdvanced glycation end products (AGEs) are a complex group of compounds produced through the non-enzymatic glycation and oxidation of proteins, lipids and nucleic acids, primarily due to aging and un...
    • 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 chain trimerization, organism-specific biosystem (from REACTOME)
      Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
    • 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
    • Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystem (from WikiPathways)
      Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystemPrimary or idiopathic focal segmental glomerulosclerosis (FSGS) a cause of nephrotic syndrome in children and adolescents, as well as an important cause of end stage renal disease in adults. FSGS is ...
    • 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% ...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    angiogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    endothelial cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    glomerular basement membrane development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glomerular basement membrane development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    basement membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    collagen type IV trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    collagen type IV trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 

    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)

    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_000092.4NP_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
      Related
      ENSP00000379866.3, ENST00000396625.4
      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 109

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

      Range
      226970293..227164559 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510565.2XP_011508867.1  collagen alpha-4(IV) chain isoform X11

      Conserved Domains (1) summary
      pfam01391
      Location:829880
      Collagen; Collagen triple helix repeat (20 copies)
    2. XM_011510570.2XP_011508872.1  collagen alpha-4(IV) chain isoform X14

      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_011510562.2XP_011508864.1  collagen alpha-4(IV) chain isoform X8

      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_011510569.2XP_011508871.1  collagen alpha-4(IV) chain isoform X14

      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)
    5. XM_017003300.1XP_016858789.1  collagen alpha-4(IV) chain isoform X14

      Conserved Domains (1) summary
      pfam01391
      Location:829880
      Collagen; Collagen triple helix repeat (20 copies)
    6. XM_011510567.2XP_011508869.1  collagen alpha-4(IV) chain isoform X12

      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)
    7. XM_011510566.2XP_011508868.1  collagen alpha-4(IV) chain isoform X12

      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)
    8. XM_011510561.2XP_011508863.1  collagen alpha-4(IV) chain isoform X8

      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
    9. XM_017003298.1XP_016858787.1  collagen alpha-4(IV) chain isoform X8

      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
    10. XM_011510560.2XP_011508862.1  collagen alpha-4(IV) chain isoform X7

      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
    11. XM_011510559.2XP_011508861.1  collagen alpha-4(IV) chain isoform X7

      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
    12. XM_005246281.3XP_005246338.1  collagen alpha-4(IV) chain isoform X1

      See identical proteins and their annotated locations for XP_005246338.1

      UniProtKB/Swiss-Prot
      P53420
      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
    13. XM_005246282.3XP_005246339.1  collagen alpha-4(IV) chain isoform X10

      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
    14. XM_011510558.2XP_011508860.1  collagen alpha-4(IV) chain isoform X4

      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
    15. XM_011510557.2XP_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
    16. XM_017003297.1XP_016858786.1  collagen alpha-4(IV) chain isoform X5

    17. XM_011510572.3XP_011508874.1  collagen alpha-4(IV) chain isoform X15

      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
    18. XM_006712246.3XP_006712309.1  collagen alpha-4(IV) chain isoform X6

      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
    19. XM_017003296.1XP_016858785.1  collagen alpha-4(IV) chain isoform X3

    20. XM_017003299.1XP_016858788.1  collagen alpha-4(IV) chain isoform X9

    21. XM_011510568.2XP_011508870.1  collagen alpha-4(IV) chain isoform X13

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

    RNA

    1. XR_001738607.1 RNA Sequence

    2. XR_001738606.1 RNA Sequence

    3. XR_001738603.1 RNA Sequence

    4. XR_922837.2 RNA Sequence

    5. XR_001738602.1 RNA Sequence

    6. XR_001738604.1 RNA Sequence

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