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col12a1 collagen, type XII, alpha 1 [ Xenopus tropicalis (tropical clawed frog) ]

Gene ID: 100495209, updated on 4-Nov-2024

Summary

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Official Symbol
col12a1provided by Xenbase
Official Full Name
collagen, type XII, alpha 1provided by Xenbase
Primary source
Xenbase:XB-GENE-1012295
See related
Ensembl:ENSXETG00000003603 AllianceGenome:Xenbase:XB-GENE-1012295
Gene type
protein coding
RefSeq status
MODEL
Organism
Xenopus tropicalis
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana
Summary
Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Human ortholog(s) of this gene implicated in Bethlem myopathy and Ullrich congenital muscular dystrophy 2. Orthologous to human COL12A1 (collagen type XII alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See col12a1 in Genome Data Viewer
Location:
chromosome: 5
Exon count:
67
Annotation release Status Assembly Chr Location
104 current UCB_Xtro_10.0 (GCF_000004195.4) 5 NC_030681.2 (90880285..91032909)
103 previous assembly Xenopus_tropicalis_v9.1 (GCF_000004195.3) 5 NC_030681.1 (82007932..82160037, complement)

Chromosome 5 - NC_030681.2Genomic Context describing neighboring genes Neighboring gene transmembrane protein 30A Neighboring gene cytochrome c oxidase subunit 7A2 Neighboring gene uncharacterized LOC108647631 Neighboring gene CD109 molecule

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by Xenbase

Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
collagen alpha-1(XII) chain
Names
collagen type XII alpha 1 chain

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Xenopus tropicalis Annotation Release 104 details...Open this link in a new tab

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

Reference UCB_Xtro_10.0 Primary Assembly

Genomic

  1. NC_030681.2 Reference UCB_Xtro_10.0 Primary Assembly

    Range
    90880285..91032909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_002936200.3 → XP_002936246.3  collagen alpha-1(XII) chain isoform X1

    UniProtKB/TrEMBL
    A0A6I8SQF8
    Conserved Domains (6) summary
    smart00060
    Location:1477 → 1549
    FN3; Fibronectin type 3 domain
    smart00210
    Location:2527 → 2718
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:1387 → 1473
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:1198 → 1361
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:336 → 415
    fn3; Fibronectin type III domain
    pfam01391
    Location:2768 → 2828
    Collagen; Collagen triple helix repeat (20 copies)

  2. XM_018094325.2 → XP_017949814.2  collagen alpha-1(XII) chain isoform X2

    UniProtKB/TrEMBL
    F7AHZ4
    Related
    ENSXETP00000007775.5, ENSXETT00000007775.5
    Conserved Domains (6) summary
    smart00060
    Location:1477 → 1549
    FN3; Fibronectin type 3 domain
    smart00210
    Location:2527 → 2718
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:1387 → 1473
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:1198 → 1361
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:336 → 415
    fn3; Fibronectin type III domain
    pfam01391
    Location:2768 → 2828
    Collagen; Collagen triple helix repeat (20 copies)

  3. XM_031901995.1 → XP_031757855.1  collagen alpha-1(XII) chain isoform X1

    UniProtKB/TrEMBL
    A0A6I8SQF8
    Related
    ENSXETP00000095381.2, ENSXETT00000084389.2
    Conserved Domains (6) summary
    smart00060
    Location:1477 → 1549
    FN3; Fibronectin type 3 domain
    smart00210
    Location:2527 → 2718
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:1387 → 1473
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:1198 → 1361
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:336 → 415
    fn3; Fibronectin type III domain
    pfam01391
    Location:2768 → 2828
    Collagen; Collagen triple helix repeat (20 copies)

  4. XM_018094326.2 → XP_017949815.2  collagen alpha-1(XII) chain isoform X3

    UniProtKB/TrEMBL
    A0A6I8QZ27, A0A8J0T166
    Related
    ENSXETP00000074885.2, ENSXETT00000091712.2
    Conserved Domains (6) summary
    smart00060
    Location:313 → 385
    FN3; Fibronectin type 3 domain
    smart00210
    Location:1363 → 1554
    TSPN; Thrombospondin N-terminal -like domains
    cd00063
    Location:223 → 309
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd01482
    Location:34 → 197
    vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
    pfam00041
    Location:780 → 859
    fn3; Fibronectin type III domain
    pfam01391
    Location:1604 → 1664
    Collagen; Collagen triple helix repeat (20 copies)
Nucleotide Protein Strain
Heading Accession and Version

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