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Aliases for COL4A4 Gene

Aliases for COL4A4 Gene

  • Collagen, Type IV, Alpha 4 2 3
  • Collagen Of Basement Membrane, Alpha-4 Chain 3
  • Collagen IV, Alpha-4 Polypeptide 3
  • Collagen Of Basement Membrane 2
  • Collagen Alpha-4(IV) Chain 3
  • Alpha-4 Chain 2
  • CA44 3

External Ids for COL4A4 Gene

Summaries for COL4A4 Gene

Entrez Gene Summary for COL4A4 Gene

  • 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]

GeneCards Summary for COL4A4 Gene

COL4A4 (Collagen, Type IV, Alpha 4) is a Protein Coding gene. Diseases associated with COL4A4 include col4a4-related nephropathy and alport syndrome, autosomal recessive. Among its related pathways are PI3K-Akt signaling pathway and Signaling by FGFR. GO annotations related to this gene include extracellular matrix structural constituent. An important paralog of this gene is COL3A1.

UniProtKB/Swiss-Prot for COL4A4 Gene

  • Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a chicken-wire meshwork together with laminins, proteoglycans and entactin/nidogen

Gene Wiki entry for COL4A4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL4A4 Gene

Genomics for COL4A4 Gene

Genomic Location for COL4A4 Gene

Start:
226,968,916 bp from pter
End:
227,164,559 bp from pter
Size:
195,644 bases
Orientation:
Minus strand

Genomic View for COL4A4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL4A4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL4A4 Gene

Regulatory Elements for COL4A4 Gene

Proteins for COL4A4 Gene

  • Protein details for COL4A4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P53420-CO4A4_HUMAN
    Recommended name:
    Collagen alpha-4(IV) chain
    Protein Accession:
    P53420
    Secondary Accessions:
    • A8MTZ1
    • Q53RW9
    • Q53S42
    • Q53WR1

    Protein attributes for COL4A4 Gene

    Size:
    1690 amino acids
    Molecular mass:
    164038 Da
    Quaternary structure:
    • There are six type IV collagen isoforms, alpha 1(IV)-alpha 6(IV), each of which can form a triple helix structure with 2 other chains to generate type IV collagen network. The alpha 3(IV) chain forms a triple helical protomer with alpha 4(IV) and alpha 5(IV); this triple helical structure dimerizes through NC1-NC1 domain interactions such that the alpha 3(IV), alpha 4(IV) and alpha 5(IV) chains of one protomer connect with the alpha 5(IV), alpha 4(IV) and alpha 3(IV) chains of the opposite protomer, respectively. Associates with LAMB2 at the neuromuscular junction and in GBM (By similarity).

neXtProt entry for COL4A4 Gene

Proteomics data for COL4A4 Gene at MOPED

Post-translational modifications for COL4A4 Gene

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains
  • The trimeric structure of the NC1 domains is stabilized by covalent bonds between Lys and Met residues.
  • Type IV collagens contain numerous cysteine residues which are involved in inter- and intramolecular disulfide bonding. 12 of these, located in the NC1 domain, are conserved in all known type IV collagens
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys1229
  • Glycosylation at Asn142 and Asn669

Other Protein References for COL4A4 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for COL4A4 Gene

Domains for COL4A4 Gene

Gene Families for COL4A4 Gene

HGNC:

Suggested Antigen Peptide Sequences for COL4A4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P53420

UniProtKB/Swiss-Prot:

CO4A4_HUMAN
Domain:
  • Alpha chains of type IV collagen have a non-collagenous domain (NC1) at their C-terminus, frequent interruptions of the G-X-Y repeats in the long central triple-helical domain (which may cause flexibility in the triple helix), and a short N-terminal triple-helical 7S domain:
    • P53420
  • Contains 1 collagen IV NC1 (C-terminal non-collagenous) domain.:
    • P53420
Family:
  • Belongs to the type IV collagen family.:
    • P53420
genes like me logo Genes that share domains with COL4A4: view

Function for COL4A4 Gene

Molecular function for COL4A4 Gene

GENATLAS Biochemistry: collagen type IV,alpha 4,glomerular basement membrane,Bowman capsule,distal TBM,neuromuscular junction,preferentially expressed early in development,suggesting a potential role in dermoepidermal junction (DEJ) formation
UniProtKB/Swiss-Prot Function: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a chicken-wire meshwork together with laminins, proteoglycans and entactin/nidogen

Gene Ontology (GO) - Molecular Function for COL4A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent IMP 17942953
genes like me logo Genes that share ontologies with COL4A4: view
genes like me logo Genes that share phenotypes with COL4A4: view

miRNA for COL4A4 Gene

miRTarBase miRNAs that target COL4A4

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for COL4A4 Gene

Localization for COL4A4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL4A4 Gene

Secreted, extracellular space, extracellular matrix, basement membrane. Note=Colocalizes with COL4A4 and COL4A5 in GBM, tubular basement membrane (TBM) and synaptic basal lamina (BL). {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL4A4 Gene COMPARTMENTS Subcellular localization image for COL4A4 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
mitochondrion 2
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for COL4A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer --
GO:0005587 collagen type IV trimer IDA 7523402
GO:0005604 basement membrane --
GO:0005605 basal lamina IDA 2211832
genes like me logo Genes that share ontologies with COL4A4: view

Pathways for COL4A4 Gene

genes like me logo Genes that share pathways with COL4A4: view

Gene Ontology (GO) - Biological Process for COL4A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007411 axon guidance TAS --
GO:0022617 extracellular matrix disassembly TAS --
GO:0030198 extracellular matrix organization TAS --
GO:0030574 collagen catabolic process TAS --
GO:0032836 glomerular basement membrane development IMP 17942953
genes like me logo Genes that share ontologies with COL4A4: view

Transcripts for COL4A4 Gene

mRNA/cDNA for COL4A4 Gene

(23) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(8) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for COL4A4 Gene

Collagen, type IV, alpha 4:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for COL4A4 Gene

No ASD Table

Relevant External Links for COL4A4 Gene

GeneLoc Exon Structure for
COL4A4
ECgene alternative splicing isoforms for
COL4A4

Expression for COL4A4 Gene

mRNA expression in normal human tissues for COL4A4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL4A4 Gene

This gene is overexpressed in Kidney - Cortex (6.1) and Pituitary (4.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for COL4A4 Gene

SOURCE GeneReport for Unigene cluster for COL4A4 Gene Hs.591645

mRNA Expression by UniProt/SwissProt for COL4A4 Gene

P53420-CO4A4_HUMAN
Tissue specificity: Alpha 3 and alpha 4 type IV collagens are colocalized and present in kidney, eye, basement membranes of lens capsule, cochlea, lung, skeletal muscle, aorta, synaptic fibers, fetal kidney and fetal lung. PubMed:8083201 reports similar levels of expression of alpha 3 and alpha 4 type IV collagens in kidney, but PubMed:7523402 reports that in kidney levels of alpha 3 type IV collagen are significantly lower than those of alpha 4 type IV collagen. Highest levels of expression of alpha 4 type IV collagen are detected in kidney, calvaria, neuroretina and cardiac muscle. Lower levels of expression are observed in brain, lung and thymus, and no expression is detected in choroid plexus, liver, adrenal, pancreas, ileum or skin.
genes like me logo Genes that share expressions with COL4A4: view

Orthologs for COL4A4 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL4A4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COL4A4 35
  • 99.21 (n)
  • 98.7 (a)
COL4A4 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COL4A4 36
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL4A4 35
  • 85.01 (n)
  • 83.27 (a)
COL4A4 36
  • 83 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col4a4 35
  • 80.81 (n)
  • 78.58 (a)
Col4a4 16
Col4a4 36
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL4A4 36
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL4A4 36
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL4A4 36
  • 58 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL4A4 36
  • 59 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii col4a4 36
  • 47 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea emb-9 37
  • 37 (a)
let-2 37
  • 56 (a)
Species with no ortholog for COL4A4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for COL4A4 Gene

ENSEMBL:
Gene Tree for COL4A4 (if available)
TreeFam:
Gene Tree for COL4A4 (if available)

Paralogs for COL4A4 Gene

Selected SIMAP similar genes for COL4A4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with COL4A4: view

Variants for COL4A4 Gene

Sequence variations from dbSNP and Humsavar for COL4A4 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs1054413 -- 227,003,003(+) CAGAT(A/G)ATAAC utr-variant-3-prime, intron-variant
rs1054415 -- 227,002,723(-) GATGA(C/G)TTCCA utr-variant-3-prime, intron-variant
rs1249622 -- 227,064,932(+) cgcgc(C/G)cgacg intron-variant
rs1317716 -- 227,103,525(-) ACATG(A/C)AGATT intron-variant
rs1317717 -- 227,103,504(-) TTTTC(A/C)ATTGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL4A4 Gene

Variant ID Type Subtype PubMed ID
esv2721548 CNV Deletion 23290073
esv25855 CNV Gain+Loss 19812545
esv2661705 CNV Deletion 23128226
nsv526108 CNV Loss 19592680
esv271089 CNV Insertion 20981092

Relevant External Links for COL4A4 Gene

HapMap Linkage Disequilibrium report
COL4A4
Human Gene Mutation Database (HGMD)
COL4A4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL4A4 Gene

Disorders for COL4A4 Gene

(1) OMIM Diseases for COL4A4 Gene (120131)

UniProtKB/Swiss-Prot

CO4A4_HUMAN
  • Alport syndrome, autosomal recessive (APSAR) [MIM:203780]: A syndrome characterized by progressive glomerulonephritis, glomerular basement membrane defects, renal failure, sensorineural deafness and specific eye abnormalities (lenticonous and macular flecks). The disorder shows considerable heterogeneity in that families differ in the age of end-stage renal disease and the occurrence of deafness. {ECO:0000269 PubMed:7987396, ECO:0000269 PubMed:9792860}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Hematuria, benign familial (BFH) [MIM:141200]: An autosomal dominant condition characterized by non-progressive isolated microscopic hematuria that does not result in renal failure. It is characterized pathologically by thinning of the glomerular basement membrane. {ECO:0000269 PubMed:11961012, ECO:0000269 PubMed:12631110, ECO:0000269 PubMed:8787673}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(5) University of Copenhagen DISEASES for COL4A4 Gene

(11) Novoseek inferred disease relationships for COL4A4 Gene

Disease -log(P) Hits PubMed IDs
alport syndrome, autosomal recessive 98.7 17
hematuria benign familial 97.6 9
alport syndrome, autosomal dominant 97.1 3
alports syndrome 96.5 22
alport syndrome, x-linked 93.1 4

Relevant External Links for COL4A4

GeneTests
COL4A4
GeneReviews
COL4A4
Genetic Association Database (GAD)
COL4A4
Human Genome Epidemiology (HuGE) Navigator
COL4A4
genes like me logo Genes that share disorders with COL4A4: view

Publications for COL4A4 Gene

  1. Mutations in the COL4A4 gene in thin basement membrane disease. (PMID: 12631110) Buzza M. … Savige J. (Kidney Int. 2003) 3 4 23 48
  2. Isolation and sequencing of cDNAs and genomic DNAs encoding the alpha 4 chain of basement membrane collagen type IV and assignment of the gene to the distal long arm of human chromosome 2. (PMID: 1429714) Kamagata Y. … Ninomiya Y. (J. Biol. Chem. 1992) 3 4 23
  3. Benign familial hematuria due to mutation of the type IV collagen alpha4 gene. (PMID: 8787673) Lemmink H.H. … Smeets H.J.M. (J. Clin. Invest. 1996) 3 4 23
  4. The clinical spectrum of type IV collagen mutations. (PMID: 9195222) Lemmink H.H. … Smeets H.J.M. (Hum. Mutat. 1997) 3 4 23
  5. Two genes, COL4A3 and COL4A4 coding for the human alpha3(IV) and alpha4(IV) collagen chains are arranged head-to-head on chromosome 2q36. (PMID: 9537506) Momota R. … Ninomiya Y. (FEBS Lett. 1998) 3 4 23

Products for COL4A4 Gene

Sources for COL4A4 Gene

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