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Kdm5c Gene Detail
Summary
  • Symbol
    Kdm5c
  • Name
    lysine (K)-specific demethylase 5C
  • Synonyms
    D930009K15Rik, Jarid1c, mKIAA0234, Smcx
  • Feature Type
    protein coding gene
  • IDs
    MGI:99781
    NCBI Gene: 20591
  • Gene Overview
    MyGene.info: KDM5C
  • Alliance
  • Transcription Start Sites
    2 TSS
Location &
Maps
more
  • Sequence Map
    ChrX:152233020-152274535 bp, + strand
  • From Ensembl annotation of GRCm38

    View this region in JBrowse

  • Genome Browsers
  • Genetic Map
    Chromosome X, 68.46 cM, cytoband F2-F4
  • Mapping Data
    16 experiments
Strain
Comparison
more
  • SNPs within 2kb
    138 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_99781
protein coding gene ChrX:152233020-152279102 (+)
129S1/SvImJ MGP_129S1SvImJ_G0036184
protein coding gene ChrX:149993319-150034803 (+)
A/J MGP_AJ_G0036160
protein coding gene ChrX:149181160-149223180 (+)
AKR/J MGP_AKRJ_G0036086
protein coding gene ChrX:154027102-154068340 (+)
BALB/cJ MGP_BALBcJ_G0036151
protein coding gene ChrX:147372749-147414323 (+)
C3H/HeJ MGP_C3HHeJ_G0035859
protein coding gene ChrX:150206552-150248463 (+)
C57BL/6NJ MGP_C57BL6NJ_G0036676
protein coding gene ChrX:154261395-154308121 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0033500
protein coding gene ChrX:140873370-140914963 (+)
CAST/EiJ MGP_CASTEiJ_G0035150
protein coding gene ChrX:129623245-129670528 (+)
CBA/J MGP_CBAJ_G0035836
protein coding gene ChrX:158801534-158848963 (+)
DBA/2J MGP_DBA2J_G0035994
protein coding gene ChrX:148249044-148290597 (+)
FVB/NJ MGP_FVBNJ_G0035928
protein coding gene ChrX:147379287-147422220 (+)
LP/J MGP_LPJ_G0036085
protein coding gene ChrX:151093888-151138478 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0035964
protein coding gene ChrX:166963870-167007608 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0036711
protein coding gene ChrX:149521933-149563431 (+)
PWK/PhJ MGP_PWKPhJ_G0034844
protein coding gene ChrX:126570152-126614332 (+)
SPRET/EiJ MGP_SPRETEiJ_G0034670
protein coding gene ChrX:130088346-130132632 (+)
WSB/EiJ MGP_WSBEiJ_G0035285
protein coding gene ChrX:147574971-147618023 (+)



Homology
more
  • Human Ortholog
    KDM5C, lysine demethylase 5C
  • Vertebrate Orthologs
    8
  • Human Ortholog
    KDM5C, lysine demethylase 5C
    Orthology source: HomoloGene, HGNC
  • Synonyms
    DXS1272E, JARID1C, MRX13, MRXJ, MRXSCJ, MRXSJ, SMCX, XE169
  • Links
    NCBI Gene ID: 8242
    neXtProt AC: NX_P41229
    UniProt: P41229

  • Chr Location
    Xp11.22; chrX:53159735-53225422 (-)  GRCh38.p7

Human Diseases
more
  • Diseases
    1 with Kdm5c mouse models; 1 with human KDM5C associations

Human Disease Mouse Models
      
IDs
View 1 model
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    18 phenotypes from 3 alleles in 3 genetic backgrounds
    13 images
    11 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
immune system
integument
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
neoplasm
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
vision/eye

Click cells to view annotations.
Male chimeras hemizygous for a gene trapped allele exhibit posterior patterning defects and abnormal heart morphology at E9.5. Chimeras hemizygous for a different gene trapped allele appear normal at E10.5.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
  • GO References
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 death
cell differentiation
cell population proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
nucleic acid-templated transcription
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
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

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
  • Tissues
  • cDNA Data
  • Literature Summary
  • Comparison Matrix
  • Interactions
    less
    Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000025332 Ensembl Gene Model | MGI Sequence Detail 41516 C57BL/6J ±  kb
    transcript ENSMUST00000112584 Ensembl | MGI Sequence Detail 5900 Not Applicable  
    polypeptide ENSMUSP00000108203 Ensembl | MGI Sequence Detail 1554 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 41
      Genomic 4
      cDNA 32
      Primer pair 4
      Other 1

      Microarray probesets 8
    Other
    Accession IDs
    less
    MGD-MRK-16567, MGI:3026968
    References
    more
    • Summaries
      All 81
      Developmental Gene Expression 20
      Diseases 1
      Gene Ontology 7
      Phenotypes 11
    • Earliest
      J:18900 Agulnik AI, et al., A mouse Y chromosome gene encoded by a region essential for spermatogenesis and expression of male-specific minor histocompatibility antigens. Hum Mol Genet. 1994 Jun;3(6):873-8
    • Latest
      J:255232 Scandaglia M, et al., Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons. Cell Rep. 2017 Oct 3;21(1):47-59

    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)
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    Funding Information
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    last database update
    10/15/2019
    MGI 6.14
    The Jackson Laboratory