Kdm5a (lysine demethylase 5A) - Rat Genome Database

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Gene: Kdm5a (lysine demethylase 5A) Chinchilla lanigera
Analyze
Symbol: Kdm5a
Name: lysine demethylase 5A
RGD ID: 9025864
Description: ENCODES a protein that exhibits chromatin binding (ortholog); chromatin DNA binding (ortholog); DNA binding (ortholog); INVOLVED IN circadian regulation of gene expression (ortholog); facultative heterochromatin formation (ortholog); male gonad development (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH alopecia areata (ortholog); ankylosing spondylitis (ortholog); breast cancer (ortholog); FOUND IN nucleus (ortholog); protein-DNA complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: lysine (K)-specific demethylase 5A; lysine-specific demethylase 5A
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554546,774,476 - 6,865,033 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554546,774,308 - 6,865,047 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Kdm5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554546,774,476 - 6,865,033 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554546,774,308 - 6,865,047 (+)NCBIChiLan1.0ChiLan1.0
KDM5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812280,057 - 389,320 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12280,057 - 389,320 (-)EnsemblGRCh38hg38GRCh38
GRCh3712389,223 - 498,486 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612259,484 - 368,881 (-)NCBINCBI36Build 36hg18NCBI36
Build 3412263,762 - 368,673NCBI
Celera121,998,056 - 2,107,462 (-)NCBICelera
Cytogenetic Map12p13.33NCBI
HuRef12242,343 - 351,308 (-)NCBIHuRef
CHM1_112388,218 - 497,621 (-)NCBICHM1_1
T2T-CHM13v2.012276,885 - 386,174 (-)NCBIT2T-CHM13v2.0
Kdm5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396120,341,060 - 120,421,535 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6120,341,085 - 120,421,535 (+)EnsemblGRCm39 Ensembl
GRCm386120,364,099 - 120,444,574 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6120,364,124 - 120,444,574 (+)EnsemblGRCm38mm10GRCm38
MGSCv376120,314,117 - 120,394,592 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366120,327,955 - 120,405,330 (+)NCBIMGSCv36mm8
Celera6122,200,858 - 122,281,399 (+)NCBICelera
Cytogenetic Map6F1NCBI
cM Map656.95NCBI
Kdm5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84155,238,124 - 155,316,121 (+)NCBIGRCr8
mRatBN7.24153,565,909 - 153,643,912 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4153,565,846 - 153,642,422 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4159,841,304 - 159,919,430 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04155,625,033 - 155,703,160 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04154,248,386 - 154,326,515 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04152,892,388 - 152,972,196 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4152,892,388 - 152,972,201 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04219,981,483 - 220,059,803 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44156,736,343 - 156,811,991 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14156,985,211 - 156,990,428 (+)NCBI
Celera4142,417,987 - 142,495,287 (+)NCBICelera
Cytogenetic Map4q42NCBI
KDM5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2105,758,829 - 5,876,875 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1125,763,791 - 5,873,625 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012342,555 - 452,161 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112307,816 - 424,135 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12319,273 - 423,634 (-)Ensemblpanpan1.1panPan2
KDM5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12742,364,606 - 42,447,839 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2742,360,456 - 42,447,821 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha274,236,467 - 4,324,130 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02742,718,407 - 42,806,253 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2742,722,124 - 42,806,202 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12742,663,789 - 42,745,548 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02742,630,772 - 42,717,451 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0273,597,143 - 3,683,827 (+)NCBIUU_Cfam_GSD_1.0
Kdm5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945108,613,494 - 108,699,241 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936606485,655 - 570,739 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936606486,424 - 570,546 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl567,629,380 - 67,715,905 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1567,628,791 - 67,716,143 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2570,002,191 - 70,049,249 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111285,206 - 381,481 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11286,728 - 381,430 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660637,960,611 - 8,056,125 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm5a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247358,530,016 - 8,631,954 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla_female_1.0 EnsemblNW_0046247358,473,897 - 8,505,745 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247358,473,778 - 8,631,964 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000018539   ⟹   ENSCLAP00000018359
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554546,774,476 - 6,865,033 (+)Ensembl
RefSeq Acc Id: XM_005396019   ⟹   XP_005396076
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554546,774,476 - 6,865,047 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005396020   ⟹   XP_005396077
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554546,792,689 - 6,865,047 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013520162   ⟹   XP_013375616
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554546,774,473 - 6,865,047 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013520163   ⟹   XP_013375617
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554546,774,474 - 6,865,047 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013520164   ⟹   XP_013375618
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554546,774,308 - 6,863,822 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_005396076   ⟸   XM_005396019
- Peptide Label: isoform X1
- UniProtKB: A0A8C2VVT0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005396077   ⟸   XM_005396020
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_013375618   ⟸   XM_013520164
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_013375616   ⟸   XM_013520162
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_013375617   ⟸   XM_013520163
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSCLAP00000018359   ⟸   ENSCLAT00000018539
Protein Domains
ARID   JmjC   JmjN   PHD-type


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000012583 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000018539 ENTREZGENE
  ENSCLAT00000018539.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.60 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  Cupin UniProtKB/TrEMBL
InterPro ARID_dom UniProtKB/TrEMBL
  ARID_dom_sf UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/TrEMBL
  KDM5A_ARID UniProtKB/TrEMBL
  KDM5A_PHD1 UniProtKB/TrEMBL
  KDM5A_PHD2 UniProtKB/TrEMBL
  KDM5A_PHD3 UniProtKB/TrEMBL
  Lys_sp_deMease-like_dom UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_C5HC2 UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene Kdm5a ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 5A UniProtKB/TrEMBL
Pfam ARID UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  PLU-1 UniProtKB/TrEMBL
  zf-C5HC2 UniProtKB/TrEMBL
PROSITE ARID UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
SMART ARID UniProtKB/TrEMBL
  BRIGHT UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
  SSF46774 UniProtKB/TrEMBL
  SSF57903 UniProtKB/TrEMBL
UniProt A0A8C2VVT0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Kdm5a  lysine demethylase 5A    lysine (K)-specific demethylase 5A  Symbol and/or name change 5135510 APPROVED