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COL26A1 collagen type XXVI alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 136227, updated on 5-Mar-2024

Summary

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Official Symbol
COL26A1provided by HGNC
Official Full Name
collagen type XXVI alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:18038
See related
Ensembl:ENSG00000160963 MIM:608927; AllianceGenome:HGNC:18038
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
EMI6; EMU2; SH2B; EMID2
Summary
This gene encodes a protein containing an emilin domain and two collagen stretches. This gene may be associated with aspirin-intolerant asthma. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2013]
Expression
Biased expression in brain (RPKM 3.1), kidney (RPKM 1.3) and 9 other tissues See more
Orthologs
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Genomic context

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See COL26A1 in Genome Data Viewer
Location:
7q22.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (101362388..101559024)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102672964..102878925)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (101006156..101202304)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100943223-100943888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100945388-100946089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100946090-100946792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100952259-100953086 Neighboring gene lncRNA p53 regulated and ESC associated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18483 Neighboring gene E2F1 mRNA stabilizing lncRNA Neighboring gene intraflagellar transport 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101015900-101016438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101029559-101030174 Neighboring gene Sharpr-MPRA regulatory region 586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:101041899-101042500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101044285-101044812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101054568-101055111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101063681-101064232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101064233-101064784 Neighboring gene NANOG hESC enhancer GRCh37_chr7:101065582-101066107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101079627-101080270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101080271-101080912 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:101081787-101082746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101104635-101105147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101128605-101129258 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101129259-101129911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101137182-101137752 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101137753-101138322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101146871-101147560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101147561-101148250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101150569-101151328 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101185407-101186075 Neighboring gene Sharpr-MPRA regulatory region 7535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101207140-101208002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101208003-101208864 Neighboring gene long intergenic non-protein coding RNA 1007 Neighboring gene uncharacterized LOC107986832

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Possible role of EMID2 on nasal polyps pathogenesis in Korean asthma patients. Pasaje CF, et al. BMC Med Genet, 2012 Jan 4. PMID 22217332, Free PMC Article
  2. Enhancer-adoption as a mechanism of human developmental disease. Lettice LA, et al. Hum Mutat, 2011 Dec. PMID 21948517
  3. A possible association of EMID2 polymorphisms with aspirin hypersensitivity in asthma. Pasaje CF, et al. Immunogenetics, 2011 Jan. PMID 21086123
  4. Type XXVI collagen, a new member of the collagen family, is specifically expressed in the testis and ovary. Sato K, et al. J Biol Chem, 2002 Oct 4. PMID 12145293
  5. Genome-wide pharmacogenomic study of citalopram-induced side effects in STAR*D. Adkins DE, et al. Transl Psychiatry, 2012 Jul 3. PMID 22760553, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. EMID2 is a novel biotherapeutic for aggressive cancers identified by in vivo screening.
    Title: EMID2 is a novel biotherapeutic for aggressive cancers identified by in vivo screening.
  2. 13 EMID2 variants were significantly associated with the presence of nasal polyps in the overall asthma group.
    Title: Possible role of EMID2 on nasal polyps pathogenesis in Korean asthma patients.
  3. EMID2 may be a susceptible genetic factor for aspirin hypersensitivity among asthmatics in Korean population.
    Title: A possible association of EMID2 polymorphisms with aspirin hypersensitivity in asthma.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: A possible association of EMID2 polymorphisms with aspirin hypersensitivity in asthma.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog
Genome-wide pharmacogenomic study of citalopram-induced side effects in STAR*D.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC129848

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in positive regulation of cell-substrate adhesion IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
located_in collagen-containing extracellular matrix HDA PubMed 
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
collagen alpha-1(XXVI) chain
Names
EMI domain containing 2
collagen, type XXVI, alpha 1
emilin and multimerin domain-containing protein 2

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.

Genomic

  1. NG_033785.2 RefSeqGene

    Range
    5056..201205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001278563.3 → NP_001265492.1  collagen alpha-1(XXVI) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_001265492.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AJ416091, BC085006, BC110393, BU845945, CX163123
    Consensus CDS
    CCDS64739.1
    UniProtKB/Swiss-Prot
    Q32M90, Q96A83
    Related
    ENSP00000318234.8, ENST00000313669.12
    Conserved Domains (1) summary
    pfam07546
    Location:54 → 122
    EMI; EMI domain

  2. NM_133457.5 → NP_597714.2  collagen alpha-1(XXVI) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_597714.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    BC085006, BC109254, BC110393, BU845945, CX163123
    UniProtKB/Swiss-Prot
    Q96A83
    Related
    ENSP00000482102.1, ENST00000613501.1
    Conserved Domains (1) summary
    pfam07546
    Location:54 → 120
    EMI; EMI domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    101362388..101559024
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011744.2 → XP_016867233.1  collagen alpha-1(XXVI) chain isoform X1

  2. XM_017011743.2 → XP_016867232.1  collagen alpha-1(XXVI) chain isoform X2

  3. XM_047419882.1 → XP_047275838.1  collagen alpha-1(XXVI) chain isoform X3

  4. XM_017011745.1 → XP_016867234.1  collagen alpha-1(XXVI) chain isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    102672964..102878925
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357233.1 → XP_054213208.1  collagen alpha-1(XXVI) chain isoform X4

    UniProtKB/Swiss-Prot
    Q32M90, Q96A83

  2. XM_054357234.1 → XP_054213209.1  collagen alpha-1(XXVI) chain isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96A83.1 GenPept UniProtKB/Swiss-Prot:Q96A83

Gene LinkOut

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