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Gene: Kdm5d (lysine demethylase 5D) Rattus norvegicus

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Symbol:

Kdm5d

Name:

lysine demethylase 5D

RGD ID:

2314436

Description:

Predicted to enable histone H3K4me/H3K4me2/H3K4me3 demethylase activity and nuclear androgen receptor binding activity. Predicted to be involved in chromatin remodeling; regulation of DNA-templated transcription; and regulation of androgen receptor signaling pathway. Predicted to act upstream of or within T cell antigen processing and presentation. Predicted to be active in chromatin and nucleus. Orthologous to human KDM5D (lysine demethylase 5D); PARTICIPATES IN histone modification pathway; INTERACTS WITH alpha-Zearalanol; atrazine; bisphenol A.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

Jarid1d; LOC103694547; lysine (K)-specific demethylase 5D; lysine-specific demethylase 5D; uncharacterized LOC103694547

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	KDM5D (lysine demethylase 5D)	HGNC	Ensembl, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Kdm5d (lysine demethylase 5D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	KDM5D (lysine demethylase 5D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LOC110257883 (lysine-specific demethylase 5D-like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	KDM5C (lysine demethylase 5C)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	KDM5D (lysine demethylase 5D)	Alliance	DIOPT (Ensembl Compara\|HGNC\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	KDM5D (lysine demethylase 5D)	Alliance	DIOPT (HGNC\|OrthoFinder\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Kdm5d (lysine demethylase 5D)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	kdm5c (lysine (K)-specific demethylase 5C)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	lid	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	rbr-2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	JHD2	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	JHD2	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	kdm5c	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	kdm5c	Alliance	DIOPT (Hieranoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	Y	551,621 - 647,742 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	Y	564,261 - 660,970 (+)	Ensembl				GRCr8
mRatBN7.2	Y	527,069 - 624,019 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	Y	530,401 - 624,018 (+)	Ensembl				mRatBN7.2
Rnor_6.0	Y	501,058 - 589,267 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	Y	505,996 - 589,267 (+)	Ensembl			rn6	Rnor6.0
Cytogenetic Map	Y	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Y-linked spermatogenic failure 2 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (ISO)

4,4'-sulfonyldiphenol (ISO)

acrolein (ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

alpha-Zearalanol (EXP)

arsenite(3-) (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

dimethylarsinic acid (ISO)

doxorubicin (ISO)

ethanol (ISO)

methidathion (ISO)

mono(2-ethylhexyl) phthalate (ISO)

ozone (ISO)

perfluorooctanoic acid (EXP)

potassium chromate (ISO)

resveratrol (ISO)

silicon dioxide (ISO)

telbivudine (EXP)

tenofovir disoproxil fumarate (EXP)

tetrachloromethane (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chromatin organization (IEA)

chromatin remodeling (IBA)

regulation of androgen receptor signaling pathway (ISO)

regulation of DNA-templated transcription (IBA)

T cell antigen processing and presentation (IEA,ISO)

Cellular Component

chromatin (IBA)

fibrillar center (ISO)

nucleus (IBA,IEA)

Molecular Function

dioxygenase activity (IEA)

DNA binding (IEA)

histone H3K4 demethylase activity (ISO)

histone H3K4me/H3K4me2/H3K4me3 demethylase activity (IBA,IEA)

metal ion binding (IEA)

nuclear androgen receptor binding (ISO)

oxidoreductase activity (IEA)

protein binding (ISO)

zinc ion binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

histone modification pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:16301625	PMID:17320160	PMID:20333173	PMID:24759410	PMID:27185910

Genomics

Comparative Map Data

Kdm5d
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	Y	551,621 - 647,742 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	Y	564,261 - 660,970 (+)	Ensembl				GRCr8
mRatBN7.2	Y	527,069 - 624,019 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	Y	530,401 - 624,018 (+)	Ensembl				mRatBN7.2
Rnor_6.0	Y	501,058 - 589,267 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	Y	505,996 - 589,267 (+)	Ensembl			rn6	Rnor6.0
Cytogenetic Map	Y	q11	NCBI

KDM5D
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	Y	19,703,865 - 19,744,726 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	Y	19,703,865 - 19,744,989 (-)	Ensembl			hg38	GRCh38
GRCh37	Y	21,865,751 - 21,906,612 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	Y	20,326,689 - 20,366,212 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	Y	20,255,427 - 20,294,949	NCBI
Celera	Y	5,866,720 - 5,906,241 (+)	NCBI		Celera
Cytogenetic Map	Y	q11.223	NCBI
HuRef	Y	15,577,021 - 15,616,789 (-)	NCBI		HuRef
T2T-CHM13v2.0	Y	20,610,415 - 20,651,276 (-)	NCBI		T2T-CHM13v2.0

Kdm5d
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	Y	897,566 - 946,316 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	Y	897,788 - 956,786 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	Y	897,566 - 943,813 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	Y	897,788 - 956,786 (+)	Ensembl			mm10	GRCm38
MGSCv37	Y	234,231 - 280,254 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	Y	234,231 - 280,254 (+)	NCBI		MGSCv36	mm8
Celera	Y	3,732,939 - 3,779,374 (+)	NCBI		Celera
Cytogenetic Map	Y	pter	NCBI

KDM5D
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	Y	36,282,210 - 36,322,055 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	Y	10,604,951 - 10,644,006 (-)	NCBI		NHGRI_mPanPan1

LOC110257883
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	Y	39,582,815 - 39,631,815 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	Y	39,582,253 - 39,631,823 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

Variants

Variants in Kdm5d
283 total Variants

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
15	9	57	152	86	87	58	74	58	6	320	161	9	133	80	46	29	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001419852	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008773689	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039100687	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063280592	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063280593	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC240535	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC241808	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC242859	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ775729	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GAPM01000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GATN01000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000022	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000086056 ⟹ ENSRNOP00000073953

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	Y	564,261 - 647,741 (+)	Ensembl
mRatBN7.2 Ensembl	Y	530,401 - 624,018 (+)	Ensembl
Rnor_6.0 Ensembl	Y	506,149 - 589,242 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000093002

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	Y	573,756 - 583,376 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000093053

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	Y	616,871 - 620,874 (+)	Ensembl
Rnor_6.0 Ensembl	Y	582,087 - 586,124 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000093125 ⟹ ENSRNOP00000076027

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	Y	505,996 - 589,267 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000126644 ⟹ ENSRNOP00000107872

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	Y	564,261 - 660,970 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000143529 ⟹ ENSRNOP00000109685

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	Y	564,261 - 647,741 (+)	Ensembl

RefSeq Acc Id:

NM_001419852 ⟹ NP_001406781

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	Y	564,486 - 647,742 (+)	NCBI
mRatBN7.2	Y	540,760 - 624,019 (+)	NCBI

RefSeq Acc Id:

XM_008773689 ⟹ XP_008771911

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	Y	556,819 - 647,742 (+)	NCBI
mRatBN7.2	Y	527,900 - 624,019 (+)	NCBI
Rnor_6.0	Y	505,875 - 589,267 (+)	NCBI

Sequence:

show sequence

TTTTCTTTGGCCGTCTCGTTTCCGCAACTTTAACTTTTACCTATGTGTGGAACGACTTCCAGGT
TAATAAATAACACTTGAAAAATATCTCGGCGGAGCAACACAACTCGTATCACATTGTGATCTAA
AAATGGTGGACCTGAACAGGGAGGTGAATATTTAAGGATGTGGAATTAAGCCGACTCTGAAATT
TGGAAAAAAATAAGTTCCTGTGGGTCATCGCAGTGAGTAGGAAATTCCATTCGCCTTTTAAAAT
CGAATCACGTTTTATAACCGCGTTTTGGGAGGACATGAAGCCAGAATCTGACGACTTTCTACCG
CCGCCCGAGTGCCCGGTGTTTGAGCCGAGTTGGGCGGAATTCCGAGATCCACTTGGCTATATAG
CTAAAATCAGACCTATTGCGGAGAAGTCAGGCATTTGCAAGATCCGCCCACCTGCGGATTGGCA
GCCTCCTTTTGCTGTAGAAATTGATAACTTCAGATTTACTCCTCGAATTCAGAGACTTAATGAA
CTGGAGGCCCAGACTAGAGTAAAACTGAACTATTTGGATCAAATTGCAAAATTCTGGGAAATTC
AAGGCTCTTCCTTAAAGATACCTAATGTGGAAAGGAAAATCTTGGACCTTTACAGCCTTAATAA
GATTGTGATAGAGGAAGGTGGATATGAAGCAATCTGCAAAGACCGTCGGTGGGCCCGTGTTGCC
CAACGCCTTAATTACCCATCAGGAAAAAACATTGGTTCCCTTCTACGGTCTCACTATGAACGGA
TCATTTACCCTTATGAAATGTTTCAGTCTGGAGCTAATCATGTGCAATGTAACACAGATCCATT
TGACAGTGAAGAAAAAGACAAGGAGTACAAACCTCATAGCATCCCTCTGAGACAGTCTGTTCAG
CCATTAAAATTCAGTTGCTACAGTAGACGAGCAAAAAGGCTACAACCTGAGCCAGAACCCACAG
AAGAAGACATTGAGAAAAACCCAGAGCTAAAAAAACTACAGATATATGGGGCAGGCCCCAAGAT
GATAGGCTTGGGCCTCATGGCAAAGGAGAAGACTCTGAGAAAGAAAGGTAGCATTCAACCAGAT
AAAGAAGAAGTGACATGCCCTGCAACTGTTATAGTGAAGGGGGAAGCCAGTGGGTTTGGAAAAG
TGACATCAGCATTTTCTGACAAGAACTTAAATCACAATTTCAAACCTTGTACTGAGATGACTAC
GCAGCTACGGAACAATCACAGCAATACCCAGTTTATGGATTCATATGTTTGCCGAATATGCTCT
CGTGGGGATGAAGATGATAGATTTCTGCTCTGTGTTGGGTGCAACGACAATTACCATATCTTTT
GCCTATTGCCACCGCTTTCTGAAGTCCCCAAGGGGGTATGGAGGTGCCCAAAGTGTATCTTAGC
GGAATGTAAGCGTCCCCTGGAAGCTTTTGGCTTTGAGCAAGCTACACAGGAGTATACGTTGCAG
AGTTTTGGTGAGATGGCTGATTCCTTCAAGGCTGACTACTTCAACATGCCTGTACATATGGTAC
CTACAGAAGTTGTGGAAAAGGAATTCTGGAGGCTGGTGAGCAGCATTGAGGAGGATGTGACAGT
TGAGTATGGAGCAGACATTCACTCCAAAGAATTTGGCAGTGGGTTTCCTGTCAACAATAGCAAA
TGGACCTTATCTCCTGAAGAAAAGGAGTATGCTGCCAGTGGTTGGAATCTCAATGTGATGCCAG
TTCTGGATCAGTCTGTTCTCTGCCACATCAATGCAGACATCTCAGGCATGAAAGTGCCTTGGTT
ATATGTGGGCATGGTGTTTTCAGCATTTTGTTGGCATATTGAGGATCACTGGAGTTACTCCATT
AACTACCTGCACTGGGGTGAACCAAAGACCTGGTATGGAGTACCTTCTCTAGCAGCAGAACACT
TGGAGGATGTTATGAAGACACTTACACCCGAGTTGTTTGACAGCCAGCCTGACCTCCTACACCA
ACTTGTCACTTTGATGAATCCCAACACTCTCATGTCACATGGAGTGCCAGTTGTTCGTACAAAC
CAGTGTGCAGGGGAATTTGTCATTACTTTCCCTCGTGCTTACCACAGTGGCTTTAATCAAGGCT
ATAACTTTGCTGAGGCAGTTAACTTTTGCACTGCTGATTGGCTACCTGTTGGACGCCAGTGTAT
TGAACACTACCGCCGACTCCGGCGCTATTGTGTCTTTTCCCATGAGGAGCTCATCTGCAAAATG
GCTGCATTCCCAGAGAAGTTGGATCTAAATCTAGCAGTGGCAGTTCACAAGGAGATGTTCATTA
TGGTACAGGAGGAGCGGCGCCTACGGAAGACCTTGTTGGAGAAGGGCATCACGGAAGCTGAGCG
AGAGGCCTTTGAGCTACTCCCAGATGATGAGCGTCAGTGCATCAAGTGTAAGACCACGTGTTTC
CTATCAGCCTTGGCCTGTTATGACTGTCCAGATGGTCTTGTCTGCCTTTCTCATATCAATGATC
TGTGCAAATGCTCAAGGAGCCGACAGTACTTACGGTACAGGTACACATTGGATGAACTGCCTGC
TATGTTACAAAAGTTGAAGATTCGGGCCGAGTCATTTGACAACTGGGCCAACAAAGTACAAGCA
GCCCTAGAGGTAGAGGACGGACGGAAACGGAGTTTTGAAGAGCTAAGAGCACTGGAAACTGAGG
CTCATGATAGACAATTTCCTAATAATGACCTGCTTCAGCGATTGAAGAAATGTCTTACTGAAGC
AGAGGCTTGCATTTCCCAAGTCCTAGAACTAGTCAATAATTCAGAGGACAGGTTAGAAACACCA
CAACTCACCCTGACTGAACTACAGATTCTTCTCAAACAGATGTGCACTCTGCCGTGTACCATAC
ATCAGATTGATGAAGTTAAGGATGTTCTGCAGCAGGTGGAGACATATCAAATTGAGACCCGTGA
GGCTCTAACTTCACTGCCTTATAGTTTAGAAATACTTCAGTCCCTGATGGAAAAGGGACAGCAG
CTTCGTGTGGAAGTTCCTGAAGCTCATCAACTTGAAGAGCTGTTGGAGCAGGCACAATGGCTAG
ATCAAGTGAAGCAGGCCCTGGCTCCCTCAGGCCAGAAACACTCTCTGGTCATCATGAAGAAACT
TTTGGTTATGGGTACCAAGTTAGCCTCCAGCCCTTCTGTGAACAAAGCTCGAGCAGAGCTACAA
GAACTGCTTACTATTGCAGAGCGTTGGGAGGAAAAGGCCCTTTTCTGCTTAGACGCTAGCCAAA
AGCATTCTCCAGCCACTTTGGAAGTTATAATACGTGAGGCAGAAAACATCCCTGTCTACTTGCC
TAACATCCAGTCTCTCAAGGAAGCTCTGACTAAGGCACAGGCTTGGATTGCTGATGTGAATGAG
ATTCAAAATGGTGATCACTACCCCTGTTTGGATGATTTGGAGGGGCTTGTAGCTGTGGGTCGGG
ATTTACCTGTGGAGCTAGAGGAACTAAAACAGCTGGAGAATCAGGTACTGACAGCACATTCCTG
GAAAGAGAAAGCTTCTAAGACTTTTCTCAAGAAGAATTCTTGCTACACACTGTTGGAGGTTCTC
TGCCCATGTGCAGATGCTGGTTCTGTCAGCACCAAGCGCAGTCGGTGGATTGAAAAGGAGATGG
GGTTATACAAATATGACACAGAATTGCTGGGGCTTTCTGCACAGGATCTCAGGGACCCAGGTTC
TGTGATCATGGCCTTTAAGGAAGGGGAAGAGAAAGAAAAAGAAGGTATCTTGCACTTGCGTCAC
ATCAACTCAACTAAGCCCAGTCCAATGTCCTCATCAATCAATGCCTCTGCAACCTCCATCTGTA
TATGTGGGCAGGTCCGTGCAGGAGTAGAAGCTCTGCGGTGTGATCTCTGTCATGACTGGTTCCA
TGGACAATGTGTGACTGTACCCCACCTACTCAGCTCCTTAAGGGCTAGTCATACCTCATCTCAA
CTGCTAGCTTGGTGGGAATGGGACACCAAATTCCTGTGCCCACTGTGTATGCGATCAAGGCGTC
CACGACTGGAGACCATATTGTCATTGCTGGTAGGACTACAGAGACTGTCTGTAAGGCTGCCTGA
GGGTGAGGCCCTACAATGCCTCACAGAGAGAGCCATTGGTTGGCAGGGCCGTGCCAGACAGGCT
CTAGCTTCTGAGAATGTGACTGCTTTGTTGAAACAGCTAGCAAAATCCCGCCAACAACTACAGG
ATGAATTGAGACATGAGAAGCCGCCTACATCTCATTCAGGTCTTCCCTCTGAGTGTCTCACAGA
GGATAGTGACAAGGATATCCTTAAGGAAGAGGAGGAGTTGGTACTAAATGAAGACATGCTGAAA
AATTCTGAGAAGATTGTTCCAAAGGAAAGTTCATGTGAAAGAGGTGAGGAACTGTTGCCTTCGC
TATTATCCCAATTAACTGGTCCTGTACTGGAACTGCCTGAAGCCACCCGGGCCCCACTAGAGGA
GCTTATGATGGAAGGAGATTTACTTGAAGTTACCCTAGATGAGAACCACAGCATTTGGCAGCTG
CTGCAGGCTGGACAGAATCCTAATCTAGAGCGGATTCATACACTTCTAGAGCTTGAGAAGCCTG
AGGACCCAAAGAATTGGTCAGAGGAACAAACACCAGAGAGGCGGCAGCGGCGAAGGCAAAAGGT
CGTTCTGAGTAGAAAGGGTGAGGATCTTACTCAAAAAGAGCTAGCATCAAAAAGAGCTAGGAGT
TCAAGGATTAAGCCTAAGGGAAAACAGTTTCAAGAGCCAATACACGGGGATAATGTGCTCTTGT
CACACCATACAGAACATACAAACATCTTAAAAGGGAACATGAACAGTGTACAAGGGAAGGATCC
AAGCCCTTCATCTACTTTTCCTTCCTTACCACCTTTGCTACATCTCTCTTATTTTCATCAGCAA
AAATTACAACAATAGTATGTGATTATTTTTTTCCTTGCTTAGTCTTTCCTTCCTTAAGCCTTTC
TCCTTTCTCTCTCCCTTTTTCTTTCCTTCCTCCTCCTTTCTCCTTTGTTGTTCCCTAGCTTCCC
TCCATTTTACTCTATTCTCTGCCCTTAATTCCCTCAGATTCCCACAAAATATTTATTCCTTACC
TACAGCTTGACTACAAATTATTTTATCCTTACTCCTAATACATGTTTATGCCTTCGTTCCTAAG
AACTATTCCATTTACATGTTTCCCAAAATTTTATCAACAATATTTCTGGAATTACTGTAGATAA
AGTGATGTTCTTGTTCTTAGTTACCTCTATTCTAATCTGGAGAAGCAAAAATAAAATTTGAGAA
TGCTAAAGTTTATTAATCTTTATTTTTAAATCCTTCATCATCCTCTGTGTAATTCCACATCGTG
TACTTATTAAAACAAGTGTTTTTTATTTTATATTTTTATTCCATTTCTTACCTTTTTCTCTTTG
GTTCACATTCTAAAAAAAATAGTATTTTGTAATTCTTAAGGAAAAAGAATACAGGAATGCAAAC
TTACCATAGTTGTTTATTTTTAATTTTGTTTCTTTTGTTGTTGGCTTTTGTTGTTGTCATTAAA
AAAATAAATAAAACATTTGCTTGGGACTGCA

hide sequence

RefSeq Acc Id:

XM_039100687 ⟹ XP_038956615

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	Y	631,315 - 647,742 (+)	NCBI
mRatBN7.2	Y	607,591 - 624,019 (+)	NCBI

RefSeq Acc Id:

XM_063280592 ⟹ XP_063136662

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	Y	551,621 - 647,742 (+)	NCBI

RefSeq Acc Id:

XM_063280593 ⟹ XP_063136663

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	Y	551,621 - 631,791 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001406781	(Get FASTA)	NCBI Sequence Viewer
	XP_008771911	(Get FASTA)	NCBI Sequence Viewer
	XP_038956615	(Get FASTA)	NCBI Sequence Viewer
	XP_063136662	(Get FASTA)	NCBI Sequence Viewer
	XP_063136663	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	ACX55121	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000073953
	ENSRNOP00000073953.2
	ENSRNOP00000107872.1
	ENSRNOP00000109685
	ENSRNOP00000109685.1
GenBank Protein	JAB84470	(Get FASTA)	NCBI Sequence Viewer
	JAC06679	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	XP_008771911 ⟸ XM_008773689
- Peptide Label:	isoform X2
- UniProtKB:	W8C8J2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MKPESDDFLPPPECPVFEPSWAEFRDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEIDNFR FTPRIQRLNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLNKIVIEEGGYEAI CKDRRWARVAQRLNYPSGKNIGSLLRSHYERIIYPYEMFQSGANHVQCNTDPFDSEEKDKEYKP HSIPLRQSVQPLKFSCYSRRAKRLQPEPEPTEEDIEKNPELKKLQIYGAGPKMIGLGLMAKEKT LRKKGSIQPDKEEVTCPATVIVKGEASGFGKVTSAFSDKNLNHNFKPCTEMTTQLRNNHSNTQF MDSYVCRICSRGDEDDRFLLCVGCNDNYHIFCLLPPLSEVPKGVWRCPKCILAECKRPLEAFGF EQATQEYTLQSFGEMADSFKADYFNMPVHMVPTEVVEKEFWRLVSSIEEDVTVEYGADIHSKEF GSGFPVNNSKWTLSPEEKEYAASGWNLNVMPVLDQSVLCHINADISGMKVPWLYVGMVFSAFCW HIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEDVMKTLTPELFDSQPDLLHQLVTLMNPNTLM SHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYNFAEAVNFCTADWLPVGRQCIEHYRRLRRYCV FSHEELICKMAAFPEKLDLNLAVAVHKEMFIMVQEERRLRKTLLEKGITEAEREAFELLPDDER QCIKCKTTCFLSALACYDCPDGLVCLSHINDLCKCSRSRQYLRYRYTLDELPAMLQKLKIRAES FDNWANKVQAALEVEDGRKRSFEELRALETEAHDRQFPNNDLLQRLKKCLTEAEACISQVLELV NNSEDRLETPQLTLTELQILLKQMCTLPCTIHQIDEVKDVLQQVETYQIETREALTSLPYSLEI LQSLMEKGQQLRVEVPEAHQLEELLEQAQWLDQVKQALAPSGQKHSLVIMKKLLVMGTKLASSP SVNKARAELQELLTIAERWEEKALFCLDASQKHSPATLEVIIREAENIPVYLPNIQSLKEALTK AQAWIADVNEIQNGDHYPCLDDLEGLVAVGRDLPVELEELKQLENQVLTAHSWKEKASKTFLKK NSCYTLLEVLCPCADAGSVSTKRSRWIEKEMGLYKYDTELLGLSAQDLRDPGSVIMAFKEGEEK EKEGILHLRHINSTKPSPMSSSINASATSICICGQVRAGVEALRCDLCHDWFHGQCVTVPHLLS SLRASHTSSQLLAWWEWDTKFLCPLCMRSRRPRLETILSLLVGLQRLSVRLPEGEALQCLTERA IGWQGRARQALASENVTALLKQLAKSRQQLQDELRHEKPPTSHSGLPSECLTEDSDKDILKEEE ELVLNEDMLKNSEKIVPKESSCERGEELLPSLLSQLTGPVLELPEATRAPLEELMMEGDLLEVT LDENHSIWQLLQAGQNPNLERIHTLLELEKPEDPKNWSEEQTPERRQRRRQKVVLSRKGEDLTQ KELASKRARSSRIKPKGKQFQEPIHGDNVLLSHHTEHTNILKGNMNSVQGKDPSPSSTFPSLPP LLHLSYFHQQKLQQ hide sequence

Ensembl Acc Id:

ENSRNOP00000076027 ⟸ ENSRNOT00000093125

Ensembl Acc Id:

ENSRNOP00000073953 ⟸ ENSRNOT00000086056

RefSeq Acc Id:	XP_038956615 ⟸ XM_039100687
- Peptide Label:	isoform X3
- UniProtKB:	V9GVE9 (UniProtKB/TrEMBL)

RefSeq Acc Id:	NP_001406781 ⟸ NM_001419852
- UniProtKB:	W8C8J2 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_063136662 ⟸ XM_063280592
- Peptide Label:	isoform X1
- UniProtKB:	A0A0G2K6V2 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_063136663 ⟸ XM_063280593
- Peptide Label:	isoform X4

Ensembl Acc Id:

ENSRNOP00000109685 ⟸ ENSRNOT00000143529

Ensembl Acc Id:

ENSRNOP00000107872 ⟸ ENSRNOT00000126644

Protein Domains

ARID JmjC JmjN PHD-type Zinc finger PHD-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-W8C8J2-F1-model_v2	AlphaFold	W8C8J2	1-1550	view protein structure

Transcriptome

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

Promoters

RGD ID:

13702079

Promoter ID:

EPDNEW_R12600

Type:

multiple initiation site

Name:

Kdm5d_1

Description:

lysine demethylase 5D

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	Y	505,989 - 506,049	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:2314436	AgrOrtholog
BioCyc Gene	G2FUF-589	BioCyc
Ensembl Genes	ENSRNOG00000060496	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000086056	ENTREZGENE
	ENSRNOT00000086056.4	UniProtKB/TrEMBL
	ENSRNOT00000126644.1	UniProtKB/TrEMBL
	ENSRNOT00000143529	ENTREZGENE
	ENSRNOT00000143529.1	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
	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	100312983	ENTREZGENE
PANTHER	LYSINE-SPECIFIC DEMETHYLASE	UniProtKB/TrEMBL
	LYSINE-SPECIFIC DEMETHYLASE 5D	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	Kdm5d	PhenoGen
PROSITE	ARID	UniProtKB/TrEMBL
	JMJC	UniProtKB/TrEMBL
	JMJN	UniProtKB/TrEMBL
	ZF_PHD_1	UniProtKB/TrEMBL
	ZF_PHD_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000060496	RatGTEx
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	A0A0G2K6V2	ENTREZGENE, UniProtKB/TrEMBL
	A0ABK0LFW9_RAT	UniProtKB/TrEMBL
	A0ABK0M063_RAT	UniProtKB/TrEMBL
	C9WPN4_RAT	UniProtKB/TrEMBL
	V9GVE9	ENTREZGENE, UniProtKB/TrEMBL
	W8C8J2	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	Kdm5d	lysine demethylase 5D	LOC103694547	uncharacterized LOC103694547	Data merged from RGD:9270267	737654	PROVISIONAL
2016-02-17	Kdm5d	lysine demethylase 5D	Kdm5d	lysine (K)-specific demethylase 5D	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2014-08-25	LOC103694547	uncharacterized LOC103694547			Symbol and Name status set to provisional	70820	PROVISIONAL
2009-11-13	Kdm5d	lysine (K)-specific demethylase 5D			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - CTD

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Imported Disease Annotations - CTD

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