Kdm5d MGI Mouse Gene Detail - MGI:99780

Kdm5d Gene Detail

Symbol

Kdm5d
Name

lysine demethylase 5D
Synonyms

HY, Jarid1d, Smcy

Feature Type

protein coding gene
IDs

MGI:99780
NCBI Gene: 20592
Alliance

gene page
Transcription Start Sites

3 TSS

Sequence Map

ChrY:897566-946316 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome Y, cytoband p
Mapping Data

8 experiments

SNPs within 2kb

40 from dbSNP Build 142
Strain Annotations

1
PCR

1
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_99780	protein coding gene	ChrY:897566-956786 (+)
129S1/SvImJ	no annotation
A/J	no annotation
AKR/J	no annotation
BALB/cJ	no annotation
C3H/HeJ	no annotation
C57BL/6NJ	no annotation
CAROLI/EiJ	no annotation
CAST/EiJ	no annotation
CBA/J	no annotation
DBA/2J	no annotation
FVB/NJ	no annotation
LP/J	no annotation
NOD/ShiLtJ	no annotation
NZO/HlLtJ	no annotation
PWK/PhJ	no annotation
SPRET/EiJ	no annotation
WSB/EiJ	no annotation

Human Ortholog

KDM5D, lysine demethylase 5D

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

KDM5D, lysine demethylase 5D
Synonyms

HY, HYA, JARID1D, SMCY
Links

HGNC:11115

NCBI Gene ID: 8284

neXtProt AC: NX_Q9BY66

UniProt: Q9BY66
Chr Location

Yq11.223; chrY:19703865-19744939 (-) GRCh38

MGI Vertebrate Homology

Kdm5d stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: KDM5D
Gene Tree

Kdm5d

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Phenotype Summary

1 phenotype from 1 allele in 1 genetic background
8 phenotype references

All Mutations and Alleles

8
Endonuclease-mediated

6
Spontaneous

1
Transgenic

1
Genomic Mutations

1 involving Kdm5d
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

73 strains or lines available

Male mice hemizygous for a null allele exhibit normal fertility.

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All GO Annotations

20
GO References

10

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

834
Tissues

74
cDNA Data

39
Literature Summary

15

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

47
RefSeq

13
UniProt

4
CCDS

CCDS30541.1

Ensembl

ENSMUSG00000056673 (Evidence)
NCBI Gene

20592

			Length	Strain/Species	Flank
genomic	20592	NCBI Gene Model \| MGI Sequence Detail	48751	C57BL/6J	± kb
transcript	NM_011419	RefSeq \| MGI Sequence Detail	7976	ZRU/MplStud
polypeptide	Q62240	UniProt \| EBI \| MGI Sequence Detail	1548	Not Applicable

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UniProt

4 Sequences
EC

1.14.11.67
InterPro Domains

IPR001606 ARID DNA-binding domain

IPR036431 ARID DNA-binding domain superfamily

IPR003347 JmjC domain

IPR003349 JmjN domain

IPR048615 Lysine-specific demethylase 5, C-terminal helical domain

IPR013637 Lysine-specific demethylase-like domain

IPR004198 Zinc finger, C5HC2-type

IPR011011 Zinc finger, FYVE/PHD-type

IPR019787 Zinc finger, PHD-finger

IPR001965 Zinc finger, PHD-type

IPR019786 Zinc finger, PHD-type, conserved site

IPR013083 Zinc finger, RING/FYVE/PHD-type

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All nucleic 66

Genomic 13

cDNA 43

Primer pair 7

Other 3

Microarray probesets 5

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MGD-MRK-16566

Summaries

All 63

Developmental Gene Expression 15

Gene Ontology 10

Phenotypes 8
Earliest

J:23697 Burgoyne PS, et al., Spermatogenic failure in male mice lacking H-Y antigen. Nature. 1986 Mar 13-19;320(6058):170-2
Latest

J:340087 Li J, et al., Histone demethylase KDM5D upregulation drives sex differences in colon cancer. Nature. 2023 Jul;619(7970):632-639

TSS for Kdm5d:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr164653	ChrY:897782-897800 (+)	225 bp
Tssr5739	ChrY:903848-903855 (+)	6,286 bp
Tssr164654	ChrY:943007-943021 (+)	45,448 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/12/2024 MGI 6.24