Kdm5a (lysine demethylase 5A) - Rat Genome Database

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Gene: Kdm5a (lysine demethylase 5A) Rattus norvegicus
Analyze
Symbol: Kdm5a
Name: lysine demethylase 5A
RGD ID: 1305429
Description: Predicted to enable several functions, including DNA binding activity; histone H3K4me/H3K4me2/H3K4me3 demethylase activity; and zinc ion binding activity. Involved in male gonad development; protein modification process; and spermatogenesis. Predicted to be part of chromatin. Predicted to be active in nucleus. Biomarker of cryptorchidism. Human ortholog(s) of this gene implicated in ankylosing spondylitis. Orthologous to human KDM5A (lysine demethylase 5A); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Jarid1a; jumonji, AT rich interactive domain 1A (Rbp2 like); LOC297563; lysine (K)-specific demethylase 5A; lysine-specific demethylase 5A; MGC189432
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IBA)
nucleus  (IBA,ISO)
protein-DNA complex  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
2. JARID1A, JMY, and PTGER4 polymorphisms are related to ankylosing spondylitis in Chinese Han patients: a case-control study. Chai W, etal., PLoS One. 2013 Sep 19;8(9):e74794. doi: 10.1371/journal.pone.0074794. eCollection 2013.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. MicroRNA-212 inhibits proliferation of gastric cancer by directly repressing retinoblastoma binding protein 2. Jiping Z, etal., J Cell Biochem. 2013 Dec;114(12):2666-72. doi: 10.1002/jcb.24613.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Distinctive changes in histone H3K4 modification mediated via Kdm5a expression in spermatogonial stem cells of cryptorchid testes. Nishio H, etal., J Urol. 2014 May;191(5 Suppl):1564-72. doi: 10.1016/j.juro.2013.10.071. Epub 2014 Mar 26.
8. Histone lysine demethylases in breast cancer. Paolicchi E, etal., Crit Rev Oncol Hematol. 2013 May;86(2):97-103. doi: 10.1016/j.critrevonc.2012.11.008. Epub 2012 Dec 23.
9. Retinoblastoma binding protein 2 (RBP2) promotes HIF-1alpha-VEGF-induced angiogenesis of non-small cell lung cancer via the Akt pathway. Qi L, etal., PLoS One. 2014 Aug 27;9(8):e106032. doi: 10.1371/journal.pone.0106032. eCollection 2014.
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Comprehensive gene review and curation RGD comprehensive gene curation
13. Deregulated expression of selected histone methylases and demethylases in prostate carcinoma. Vieira FQ, etal., Endocr Relat Cancer. 2013 Dec 16;21(1):51-61. doi: 10.1530/ERC-13-0375. Print 2014 Feb.
14. Abnormal epigenetic modifications in peripheral blood mononuclear cells from patients with alopecia areata. Zhao M, etal., Br J Dermatol. 2012 Feb;166(2):226-73. doi: 10.1111/j.1365-2133.2011.10646.x. Epub 2012 Jan 9.
Additional References at PubMed
PMID:11358960   PMID:11445587   PMID:12477932   PMID:15632090   PMID:15640446   PMID:18270511   PMID:18483221   PMID:19430464   PMID:20064375   PMID:21960634   PMID:27499454   PMID:29212818  
PMID:37084543  


Genomics

Comparative Map Data
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
(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
(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
(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

Variants

.
Variants in Kdm5a
252 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:154
Count of miRNA genes:120
Interacting mature miRNAs:127
Transcripts:ENSRNOT00000056198
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4148423102157580971Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4153031106158841762Rat

Markers in Region
RH142775  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24153,639,189 - 153,639,323 (+)MAPPERmRatBN7.2
Rnor_6.04152,967,474 - 152,967,607NCBIRnor6.0
Rnor_5.04220,055,081 - 220,055,214UniSTSRnor5.0
RGSC_v3.44156,809,560 - 156,809,693UniSTSRGSC3.4
Celera4142,490,565 - 142,490,698UniSTS
RH 3.4 Map4989.3UniSTS
Cytogenetic Map4q42UniSTS
AW524686  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24153,642,083 - 153,642,262 (+)MAPPERmRatBN7.2
Rnor_6.04152,970,368 - 152,970,546NCBIRnor6.0
Rnor_5.04220,057,975 - 220,058,153UniSTSRnor5.0
RGSC_v3.44156,812,454 - 156,812,632UniSTSRGSC3.4
Celera4142,493,459 - 142,493,637UniSTS
RH 3.4 Map4987.8UniSTS
Cytogenetic Map4q42UniSTS
AA926315  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24153,575,145 - 153,575,334 (+)MAPPERmRatBN7.2
Rnor_6.04152,901,624 - 152,901,812NCBIRnor6.0
Rnor_5.04219,990,719 - 219,990,907UniSTSRnor5.0
RGSC_v3.44156,745,363 - 156,745,551UniSTSRGSC3.4
Celera4142,427,223 - 142,427,411UniSTS
RH 3.4 Map4990.0UniSTS
Cytogenetic Map4q42UniSTS
RH124853  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24153,629,839 - 153,629,929 (+)MAPPERmRatBN7.2
Rnor_6.04152,958,124 - 152,958,213NCBIRnor6.0
Rnor_5.04220,045,731 - 220,045,820UniSTSRnor5.0
RGSC_v3.44156,800,210 - 156,800,299UniSTSRGSC3.4
Celera4142,481,215 - 142,481,304UniSTS
Cytogenetic Map4q42UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 38 22 19 22 8 8 74 34 38 11 8
Low 9 19 19 19 3 1 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000056198   ⟹   ENSRNOP00000053044
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4152,892,388 - 152,925,928 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075895   ⟹   ENSRNOP00000068325
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4153,565,846 - 153,642,422 (+)Ensembl
Rnor_6.0 Ensembl4152,892,388 - 152,972,201 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076032   ⟹   ENSRNOP00000068178
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4152,945,760 - 152,967,361 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079090   ⟹   ENSRNOP00000072912
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4153,565,846 - 153,633,285 (+)Ensembl
Rnor_6.0 Ensembl4152,892,599 - 152,966,068 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090218   ⟹   ENSRNOP00000068854
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4153,565,846 - 153,642,422 (+)Ensembl
Rnor_6.0 Ensembl4152,892,388 - 152,972,196 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093794   ⟹   ENSRNOP00000080116
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4153,565,846 - 153,642,422 (+)Ensembl
RefSeq Acc Id: NM_001277177   ⟹   NP_001264106
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84155,238,124 - 155,316,121 (+)NCBI
mRatBN7.24153,565,909 - 153,643,912 (+)NCBI
Rnor_6.04152,892,388 - 152,972,196 (+)NCBI
Rnor_5.04219,981,483 - 220,059,803 (+)NCBI
Celera4142,417,987 - 142,495,287 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001277178   ⟹   NP_001264107
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84155,238,124 - 155,271,345 (+)NCBI
mRatBN7.24153,565,909 - 153,599,132 (+)NCBI
Rnor_6.04152,892,388 - 152,925,928 (+)NCBI
Rnor_5.04219,981,483 - 220,059,803 (+)NCBI
Celera4142,417,987 - 142,451,208 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001264106   ⟸   NM_001277177
- Peptide Label: isoform 1
- UniProtKB: A0A0G2K454 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001264107   ⟸   NM_001277178
- Peptide Label: isoform 2
- UniProtKB: B5DFF8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072912   ⟸   ENSRNOT00000079090
RefSeq Acc Id: ENSRNOP00000068854   ⟸   ENSRNOT00000090218
RefSeq Acc Id: ENSRNOP00000068325   ⟸   ENSRNOT00000075895
RefSeq Acc Id: ENSRNOP00000053044   ⟸   ENSRNOT00000056198
RefSeq Acc Id: ENSRNOP00000068178   ⟸   ENSRNOT00000076032
RefSeq Acc Id: ENSRNOP00000080116   ⟸   ENSRNOT00000093794
Protein Domains
ARID   JmjC   JmjN   PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JTU9-F1-model_v2 AlphaFold A0A0G2JTU9 1-1690 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13693355
Promoter ID:EPDNEW_R3878
Type:initiation region
Name:Kdm5a_1
Description:lysine demethylase 5A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3879  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04152,892,360 - 152,892,420EPDNEW
RGD ID:13693368
Promoter ID:EPDNEW_R3879
Type:initiation region
Name:Kdm5a_2
Description:lysine demethylase 5A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3878  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04152,892,601 - 152,892,661EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305429 AgrOrtholog
BioCyc Gene G2FUF-43200 BioCyc
Ensembl Genes ENSRNOG00000010591 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075895 ENTREZGENE
  ENSRNOT00000075895.3 UniProtKB/TrEMBL
  ENSRNOT00000079090.2 UniProtKB/TrEMBL
  ENSRNOT00000090218.2 UniProtKB/TrEMBL
  ENSRNOT00000093794.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.60 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  Cupin UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7936650 IMAGE-MGC_LOAD
InterPro ARID/BRIGHT_DNA-bd UniProtKB/TrEMBL
  ARID_dom_sf UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/TrEMBL
  KDM5A_ARID UniProtKB/TrEMBL
  KDM5A_PHD1 UniProtKB/TrEMBL
  KDM5A_PHD2 UniProtKB/TrEMBL
  KDM5A_PHD3 UniProtKB/TrEMBL
  PLU-1 UniProtKB/TrEMBL
  TF_JmjC_AAH UniProtKB/TrEMBL
  TF_JmjN 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
MGC_CLONE MGC:124723 IMAGE-MGC_LOAD
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
PhenoGen Kdm5a PhenoGen
PROSITE ARID UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010591 RatGTEx
SMART ARID UniProtKB/TrEMBL
  BRIGHT UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
Superfamily-SCOP ARID UniProtKB/TrEMBL
  Clavaminate synthase-like UniProtKB/TrEMBL
  FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt A0A096MJZ8_RAT UniProtKB/TrEMBL
  A0A0G2JTU9_RAT UniProtKB/TrEMBL
  A0A0G2K454 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZPK6_RAT UniProtKB/TrEMBL
  B5DFF8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kdm5a  lysine demethylase 5A  Kdm5a  lysine (K)-specific demethylase 5A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-18 Kdm5a  lysine (K)-specific demethylase 5A  Jarid1a  jumonji, AT rich interactive domain 1A (Rbp2 like)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Jarid1a  jumonji, AT rich interactive domain 1A (Rbp2 like)   Jarid1a_predicted  jumonji, AT rich interactive domain 1A (Rbp2 like) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Jarid1a_predicted  jumonji, AT rich interactive domain 1A (Rbp2 like) (predicted)      Symbol and Name status set to approved 70820 APPROVED