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COL2A1 collagen type II alpha 1 chain [ Bubalus bubalis (water buffalo) ]

Gene ID: 102403678, updated on 10-Mar-2024

Summary

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Gene symbol
COL2A1
Gene description
collagen type II alpha 1 chain
See related
EnsemblRapid:ENSBALG00030020787
Gene type
protein coding
RefSeq status
MODEL
Organism
Bubalus bubalis
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bubalus
Orthologs
human mouse all
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Genomic context

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See COL2A1 in Genome Data Viewer
Location:
chromosome: 4
Exon count:
54
Annotation release Status Assembly Chr Location
103 current NDDB_SH_1 (GCF_019923935.1) 4 NC_059160.1 (87979711..88010135, complement)
102 previous assembly NDDB_DH_1 (GCF_019923925.1) 4 NC_058346.1 (86902019..86932444, complement)

Chromosome 4 - NC_059160.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC123333293 Neighboring gene transmembrane protein 106C Neighboring gene SUMO specific peptidase 1 Neighboring gene phosphofructokinase, muscle

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. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. Deng T, et al. PLoS One, 2016. PMID 26766209, Free PMC Article
  2. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
  3. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables extracellular matrix structural constituent IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables protein binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen type II trimer IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
collagen alpha-1(II) chain

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Bubalus bubalis Annotation Release 103 details...Open this link in a new tab

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

Reference NDDB_SH_1 Primary Assembly

Genomic

  1. NC_059160.1 Reference NDDB_SH_1 Primary Assembly

    Range
    87979711..88010135 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006059438.4 → XP_006059500.1  collagen alpha-1(II) chain isoform X1

    Related
    ENSBALP00030039135.1, ENSBALT00030058245.1
    Conserved Domains (3) summary
    pfam01391
    Location:801 → 860
    Collagen; Collagen triple helix repeat (20 copies)
    pfam00093
    Location:34 → 89
    VWC; von Willebrand factor type C domain
    pfam01410
    Location:1254 → 1486
    COLFI; Fibrillar collagen C-terminal domain

  2. XM_006059439.4 → XP_006059501.1  collagen alpha-1(II) chain isoform X2

    Related
    ENSBALP00030039263.1, ENSBALT00030058428.1
    Conserved Domains (2) summary
    pfam01391
    Location:732 → 791
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:1185 → 1417
    COLFI; Fibrillar collagen C-terminal domain
Nucleotide Protein
Heading Accession and Version

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