U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    col12a1b collagen, type XII, alpha 1b [ Danio rerio (zebrafish) ]

    Gene ID: 562946, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    col12a1bprovided by ZNC
    Official Full Name
    collagen, type XII, alpha 1bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-120215-116
    See related
    Ensembl:ENSDARG00000019601 AllianceGenome:ZFIN:ZDB-GENE-120215-116
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    col12a1; si:ch211-106k22.1
    Summary
    Acts upstream of or within regeneration and regulation of axon regeneration. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix. Is expressed in trunk. 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, Dec 2024]
    Orthologs
    all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See col12a1b in Genome Data Viewer
    Location:
    chromosome: 20
    Exon count:
    78
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (49450996..49683967, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (49647149..49869321, complement)

    Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene CD109 molecule Neighboring gene uncharacterized LOC137488601 Neighboring gene uncharacterized LOC137488703 Neighboring gene cytochrome c oxidase subunit 7A2b

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Zebrafish collagen XIV is transiently expressed in epithelia and is required for proper function of certain basement membranes. Bader HL, et al. J Biol Chem, 2013 Mar 8. PMID 23325806, Free PMC Article
    2. Collagen XII Contributes to Epicardial and Connective Tissues in the Zebrafish Heart during Ontogenesis and Regeneration. Marro J, et al. PLoS One, 2016. PMID 27783651, Free PMC Article
    3. Transcriptomic underpinnings of high and low mirror aggression zebrafish behaviours. Reichmann F, et al. BMC Biol, 2022 May 2. PMID 35501893, Free PMC Article
    4. Transient fibrosis resolves via fibroblast inactivation in the regenerating zebrafish heart. Sánchez-Iranzo H, et al. Proc Natl Acad Sci U S A, 2018 Apr 17. PMID 29610343, Free PMC Article
    5. Cell differentiation and matrix organization are differentially affected during bone formation in osteogenesis imperfecta zebrafish models with different genetic defects impacting collagen type I structure. Daponte V, et al. Matrix Biol, 2023 Aug. PMID 37336269

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of_or_within regeneration IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of axon regeneration IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    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

    Go to the top of the page Help
    Preferred Names
    collagen alpha-1(XII) chain; collagen, type XII, alpha 1b
    Names
    collagen, type XII, alpha 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007131.7 Reference GRCz11 Primary Assembly

      Range
      49450996..49683967 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021468712.2 → XP_021324387.1  collagen alpha-1(XII) chain isoform X5

      UniProtKB/TrEMBL
      A0A8M9P340
      Conserved Domains (7) summary
      pfam01391
      Location:2192 → 2242
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:402 → 480
      FN3; Fibronectin type 3 domain
      smart00210
      Location:1903 → 2097
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:1499 → 1576
      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:33 → 196
      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:592 → 670
      fn3; Fibronectin type III domain
      cl21522
      Location:312 → 393
      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 ...

    2. XM_017352646.3 → XP_017208135.2  collagen alpha-1(XII) chain isoform X3

      UniProtKB/TrEMBL
      A0A8M6Z2U2, A0A8M6Z3F3
      Related
      ENSDARP00000009356.7, ENSDART00000025926.9
      Conserved Domains (7) summary
      pfam01391
      Location:3351 → 3401
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:1568 → 1646
      FN3; Fibronectin type 3 domain
      smart00210
      Location:3062 → 3256
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:2658 → 2735
      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:1199 → 1362
      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:1751 → 1829
      fn3; Fibronectin type III domain
      cl21522
      Location:1478 → 1559
      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 ...

    3. XM_017352645.3 → XP_017208134.2  collagen alpha-1(XII) chain isoform X2

      UniProtKB/TrEMBL
      A0A8M6YWS8, A0A8M6Z2U2
      Conserved Domains (7) summary
      pfam01391
      Location:3355 → 3405
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:1568 → 1646
      FN3; Fibronectin type 3 domain
      smart00210
      Location:3066 → 3260
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:2662 → 2739
      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:1199 → 1362
      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:1758 → 1836
      fn3; Fibronectin type III domain
      cl21522
      Location:1478 → 1559
      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 ...

    4. XM_017352644.3 → XP_017208133.2  collagen alpha-1(XII) chain isoform X1

      UniProtKB/TrEMBL
      A0A8M6YUY1, A0A8M6Z2U2
      Conserved Domains (7) summary
      pfam01391
      Location:3358 → 3408
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:1568 → 1646
      FN3; Fibronectin type 3 domain
      smart00210
      Location:3069 → 3263
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:2665 → 2742
      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:1199 → 1362
      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:1758 → 1836
      fn3; Fibronectin type III domain
      cl21522
      Location:1478 → 1559
      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 ...

    5. XM_017352647.3 → XP_017208136.2  collagen alpha-1(XII) chain isoform X4

      UniProtKB/TrEMBL
      A0A8M6YUB5, A0A8M6Z2U2
      Conserved Domains (7) summary
      pfam01391
      Location:3358 → 3408
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:1568 → 1646
      FN3; Fibronectin type 3 domain
      smart00210
      Location:3069 → 3263
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:2665 → 2742
      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:1199 → 1362
      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:1758 → 1836
      fn3; Fibronectin type III domain
      cl21522
      Location:1478 → 1559
      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 ...
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials
    Tools