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Col4a6 collagen, type IV, alpha 6 [ Mus musculus (house mouse) ]

Gene ID: 94216, updated on 25-Jan-2022

Summary

Official Symbol
Col4a6provided by MGI
Official Full Name
collagen, type IV, alpha 6provided by MGI
Primary source
MGI:MGI:2152695
See related
Ensembl:ENSMUSG00000031273 AllianceGenome:MGI:2152695
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
BB116301
Summary
An extracellular matrix structural constituent. Acts upstream of or within cellular response to amino acid stimulus; collagen-activated tyrosine kinase receptor signaling pathway; and extracellular matrix organization. Located in basement membrane. Part of collagen type IV trimer. Is expressed in several structures, including bone; meninges; oral region epithelium; sensory organ; and trunk. Human ortholog(s) of this gene implicated in AMME complex and X-linked deafness 6. Orthologous to human COL4A6 (collagen type IV alpha 6 chain). [provided by Alliance of Genome Resources, Nov 2021]
Expression
Broad expression in bladder adult (RPKM 12.0), ovary adult (RPKM 3.7) and 15 other tissues See more
Orthologs
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Genomic context

See Col4a6 in Genome Data Viewer
Location:
X; X F1- F2
Exon count:
46
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) X NC_000086.8 (139948399..140257091, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (141165403..141474095, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) X NC_000086.6 (137599946..137908619, complement)

Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene V-set and immunoglobulin domain containing 1 Neighboring gene proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 Neighboring gene autophagy related 4A, cysteine peptidase Neighboring gene predicted gene, 39539 Neighboring gene prohibitin pseudogene Neighboring gene collagen, type IV, alpha 5 Neighboring gene predicted gene 15295 Neighboring gene insulin receptor substrate 4

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Component Evidence Code Pubs
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 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-6(IV) chain
Names
procollagen, type IV, alpha 6

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_053185.2NP_444415.2  collagen alpha-6(IV) chain precursor

    Status: VALIDATED

    Source sequence(s)
    AB041351, AL691493, CF538953, CF539876, CF747750, CN535678, CV555853
    Consensus CDS
    CCDS41153.1
    UniProtKB/TrEMBL
    B1AVK5, Q9ESQ1
    Related
    ENSMUSP00000098765.3, ENSMUST00000101205.3
    Conserved Domains (2) summary
    pfam01391
    Location:14011460
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:15761688
    C4; C-terminal tandem repeated domain in type 4 procollagen

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000086.8 Reference GRCm39 C57BL/6J

    Range
    139948399..140257091 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011247883.4XP_011246185.1  collagen alpha-6(IV) chain isoform X1

    Conserved Domains (3) summary
    pfam01391
    Location:13771436
    Collagen; Collagen triple helix repeat (20 copies)
    pfam09606
    Location:10801439
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam01413
    Location:15521664
    C4; C-terminal tandem repeated domain in type 4 procollagen

RNA

  1. XR_003953035.1 RNA Sequence

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