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jmjd1c jumonji domain containing 1C [ Xenopus tropicalis (tropical clawed frog) ]

Gene ID: 100487525, updated on 4-Nov-2024

Summary

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Official Symbol
jmjd1cprovided by Xenbase
Official Full Name
jumonji domain containing 1Cprovided by Xenbase
Primary source
Xenbase:XB-GENE-1008867
See related
Ensembl:ENSXETG00000007684 AllianceGenome:Xenbase:XB-GENE-1008867
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
Also known as
trip8
Summary
Predicted to enable chromatin DNA binding activity; histone H3K9 demethylase activity; and transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within demethylation. Predicted to be located in chromatin. Predicted to be part of histone deacetylase complex. Orthologous to human JMJD1C (jumonji domain containing 1C). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See jmjd1c in Genome Data Viewer
Location:
chromosome: 7
Exon count:
27
Annotation release Status Assembly Chr Location
104 current UCB_Xtro_10.0 (GCF_000004195.4) 7 NC_030683.2 (18049504..18235442, complement)
103 previous assembly Xenopus_tropicalis_v9.1 (GCF_000004195.3) 7 NC_030683.1 (9248000..9408340)

Chromosome 7 - NC_030683.2Genomic Context describing neighboring genes Neighboring gene early growth response 2 Neighboring gene nuclear receptor binding factor 2 Neighboring gene uncharacterized LOC108648145 Neighboring gene uncharacterized LOC105947747

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

Function Evidence Code Pubs
enables chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K9 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within demethylation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone deacetylase complex IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
probable JmjC domain-containing histone demethylation protein 2C

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_030683.2 Reference UCB_Xtro_10.0 Primary Assembly

    Range
    18049504..18235442 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_031905352.1 → XP_031761212.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

    UniProtKB/TrEMBL
    A0A803K3U5, A0A8J1JTJ7
    Related
    ENSXETP00000114995.1, ENSXETT00000118478.1
    Conserved Domains (3) summary
    smart00558
    Location:2263 → 2335
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl40423
    Location:2376 → 2466
    cupin_RmlC-like; RmlC-like cupin superfamily
    cl41729
    Location:1115 → 1249
    KLF1_2_4_N; N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins

  2. XM_031905351.1 → XP_031761211.1  probable JmjC domain-containing histone demethylation protein 2C isoform X2

    UniProtKB/TrEMBL
    A0A803K3U5, A0A8J1JXC1
    Conserved Domains (3) summary
    smart00558
    Location:2265 → 2337
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl40423
    Location:2378 → 2468
    cupin_RmlC-like; RmlC-like cupin superfamily
    cl41729
    Location:1118 → 1252
    KLF1_2_4_N; N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins

  3. XM_031905350.1 → XP_031761210.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

    UniProtKB/TrEMBL
    A0A803K3U5, A0A8J1JW00
    Conserved Domains (3) summary
    smart00558
    Location:2266 → 2338
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl40423
    Location:2379 → 2469
    cupin_RmlC-like; RmlC-like cupin superfamily
    cl41729
    Location:1118 → 1252
    KLF1_2_4_N; N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins

  4. XM_031905353.1 → XP_031761213.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

    UniProtKB/TrEMBL
    A0A7D9NLN0, A0A803JFM0
    Related
    ENSXETP00000016739.5, ENSXETT00000016739.5
    Conserved Domains (3) summary
    smart00558
    Location:2079 → 2151
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl40423
    Location:2192 → 2282
    cupin_RmlC-like; RmlC-like cupin superfamily
    cl41729
    Location:931 → 1065
    KLF1_2_4_N; N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins

  5. XM_031905354.1 → XP_031761214.1  probable JmjC domain-containing histone demethylation protein 2C isoform X5

    UniProtKB/TrEMBL
    A0A6I8QSX2, A0A6I8QUV0, A0A803JFM0
    Related
    ENSXETP00000072297.2, ENSXETT00000078258.2
    Conserved Domains (3) summary
    smart00558
    Location:2082 → 2154
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl40423
    Location:2195 → 2285
    cupin_RmlC-like; RmlC-like cupin superfamily
    cl41729
    Location:934 → 1068
    KLF1_2_4_N; N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins
Nucleotide Protein Strain
Heading Accession and Version

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