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kdm5a lysine demethylase 5A [ Xenopus tropicalis (tropical clawed frog) ]

Gene ID: 100492348, updated on 4-Nov-2024

Summary

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Official Symbol
kdm5aprovided by Xenbase
Official Full Name
lysine demethylase 5Aprovided by Xenbase
Primary source
Xenbase:XB-GENE-996070
See related
Ensembl:ENSXETG00000003642 AllianceGenome:Xenbase:XB-GENE-996070
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
jarid1a
Summary
Predicted to enable DNA binding activity; histone H3K4me/H3K4me2/H3K4me3 demethylase activity; and metal ion binding activity. Predicted to act upstream of or within chromatin organization. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in ankylosing spondylitis. Orthologous to human KDM5A (lysine demethylase 5A). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See kdm5a in Genome Data Viewer
Location:
chromosome: 3
Exon count:
28
Annotation release Status Assembly Chr Location
104 current UCB_Xtro_10.0 (GCF_000004195.4) 3 NC_030679.2 (9937959..9969213)
103 previous assembly Xenopus_tropicalis_v9.1 (GCF_000004195.3) Unplaced Scaffold NW_016683455.1 (76101..108201)

Chromosome 3 - NC_030679.2Genomic Context describing neighboring genes Neighboring gene beta-1,4-N-acetyl-galactosaminyl transferase 3 Neighboring gene serine/threonine-protein kinase 3-like Neighboring gene coiled-coil domain containing 77 Neighboring gene solute carrier family 6 (neurotransmitter transporter), member 13 Neighboring gene solute carrier family 6 (neurotransmitter transporter), member 12

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 DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
lysine-specific demethylase 5A
Names
lysine (K)-specific demethylase 5A

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_030679.2 Reference UCB_Xtro_10.0 Primary Assembly

    Range
    9937959..9969213
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_031898637.1 → XP_031754497.1  lysine-specific demethylase 5A isoform X1

    UniProtKB/TrEMBL
    A0A6I8RI64, A0A8J1J9F8
    Conserved Domains (8) summary
    smart00545
    Location:12 → 53
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15602
    Location:288 → 336
    PHD1_KDM5A; PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A)
    cd15606
    Location:1154 → 1206
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15686
    Location:1599 → 1650
    PHD3_KDM5A; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A)
    cd16873
    Location:78 → 169
    ARID_KDM5A; ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A)
    pfam02373
    Location:463 → 579
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:669 → 721
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:734 → 1064
    PLU-1; PLU-1-like protein

  2. XM_031898640.1 → XP_031754500.1  lysine-specific demethylase 5A isoform X3

    UniProtKB/TrEMBL
    A0A6I8RI64, A0A8J1JBW6
    Related
    ENSXETP00000098457.2, ENSXETT00000092281.2
    Conserved Domains (8) summary
    smart00545
    Location:12 → 53
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15602
    Location:288 → 336
    PHD1_KDM5A; PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A)
    cd15606
    Location:1154 → 1206
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15686
    Location:1597 → 1648
    PHD3_KDM5A; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A)
    cd16873
    Location:78 → 169
    ARID_KDM5A; ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A)
    pfam02373
    Location:463 → 579
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:669 → 721
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:734 → 1064
    PLU-1; PLU-1-like protein

  3. XM_031898641.1 → XP_031754501.1  lysine-specific demethylase 5A isoform X4

    UniProtKB/TrEMBL
    A0A6I8RI64, A0A8J1JD02
    Related
    ENSXETP00000081318.2, ENSXETT00000079955.2
    Conserved Domains (8) summary
    smart00545
    Location:12 → 53
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15602
    Location:288 → 336
    PHD1_KDM5A; PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A)
    cd15606
    Location:1154 → 1206
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15686
    Location:1551 → 1602
    PHD3_KDM5A; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A)
    cd16873
    Location:78 → 169
    ARID_KDM5A; ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A)
    pfam02373
    Location:463 → 579
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:669 → 721
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:734 → 1064
    PLU-1; PLU-1-like protein

  4. XM_031898638.1 → XP_031754498.1  lysine-specific demethylase 5A isoform X2

    UniProtKB/TrEMBL
    A0A6I8RI64, A0A6I8SFL3
    Related
    ENSXETP00000097057.2, ENSXETT00000075703.2
    Conserved Domains (8) summary
    smart00545
    Location:12 → 53
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15602
    Location:288 → 336
    PHD1_KDM5A; PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A)
    cd15606
    Location:1153 → 1205
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15686
    Location:1598 → 1649
    PHD3_KDM5A; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A)
    cd16873
    Location:78 → 169
    ARID_KDM5A; ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A)
    pfam02373
    Location:463 → 579
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:669 → 721
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:734 → 1063
    PLU-1; PLU-1-like protein
Nucleotide Protein Strain
Heading Accession and Version

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