KDM7A (lysine demethylase 7A) - Rat Genome Database

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Gene: KDM7A (lysine demethylase 7A) Canis lupus familiaris
Analyze
Symbol: KDM7A
Name: lysine demethylase 7A
RGD ID: 12336054
Description: ENCODES a protein that exhibits 2-oxoglutarate-dependent dioxygenase activity (inferred); dioxygenase activity (inferred); histone demethylase activity (inferred); INVOLVED IN chromatin organization (inferred); chromatin remodeling (inferred); positive regulation of DNA-templated transcription (inferred); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH genetic disease (ortholog); melanoma (ortholog); pleomorphic xanthoastrocytoma (ortholog); FOUND IN nucleolus (inferred); nucleoplasm (inferred); nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: JHDM1D; jumonji C domain containing histone demethylase 1 homolog D; lysine-specific demethylase 7A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1168,737,670 - 8,820,925 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl168,740,492 - 8,814,402 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha169,583,276 - 9,664,675 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0168,660,254 - 8,741,637 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl168,660,194 - 8,737,535 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1168,610,970 - 8,692,356 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0168,455,403 - 8,536,816 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0168,524,015 - 8,605,439 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleolus  (IEA)
nucleoplasm  (IEA)
nucleus  (IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
KDM7A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1168,737,670 - 8,820,925 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl168,740,492 - 8,814,402 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha169,583,276 - 9,664,675 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0168,660,254 - 8,741,637 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl168,660,194 - 8,737,535 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1168,610,970 - 8,692,356 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0168,455,403 - 8,536,816 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0168,524,015 - 8,605,439 (+)NCBIUU_Cfam_GSD_1.0
KDM7A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387140,084,746 - 140,176,983 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7140,084,746 - 140,176,983 (-)EnsemblGRCh38hg38GRCh38
GRCh377139,784,546 - 139,876,783 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367139,431,015 - 139,523,210 (-)NCBINCBI36Build 36hg18NCBI36
Celera7134,506,404 - 134,598,541 (-)NCBICelera
Cytogenetic Map7q34NCBI
HuRef7134,078,435 - 134,132,803 (-)NCBIHuRef
CHM1_17139,719,043 - 139,811,668 (-)NCBICHM1_1
T2T-CHM13v2.07141,398,329 - 141,490,536 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27139,113,396 - 139,205,589 (-)NCBI
Kdm7a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39639,113,554 - 39,183,707 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl639,113,557 - 39,183,723 (-)EnsemblGRCm39 Ensembl
GRCm38639,136,620 - 39,206,773 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl639,136,623 - 39,206,789 (-)EnsemblGRCm38mm10GRCm38
MGSCv37639,086,619 - 39,156,772 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36639,068,726 - 39,136,218 (-)NCBIMGSCv36mm8
Celera639,120,728 - 39,190,894 (-)NCBICelera
Cytogenetic Map6B1NCBI
cM Map617.87NCBI
Kdm7a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8468,866,263 - 68,992,979 (-)NCBIGRCr8
mRatBN7.2467,899,407 - 67,974,264 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl467,904,307 - 67,966,998 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0466,915,603 - 66,957,971 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl466,922,013 - 66,955,732 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0466,720,232 - 66,786,800 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera462,912,406 - 62,952,948 (-)NCBICelera
Cytogenetic Map4q23NCBI
Kdm7a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554943,030,133 - 3,104,215 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554943,018,395 - 3,110,528 (+)NCBIChiLan1.0ChiLan1.0
KDM7A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26176,878,180 - 176,977,246 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1728,888,543 - 28,984,449 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07132,022,983 - 132,118,881 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17144,503,862 - 144,561,227 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7144,510,213 - 144,561,230 (-)Ensemblpanpan1.1panPan2
Kdm7a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511814,913,965 - 14,969,135 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365924,257,113 - 4,298,903 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365924,250,658 - 4,305,838 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM7A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl189,581,384 - 9,664,748 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1189,581,468 - 9,664,750 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21810,087,583 - 10,169,392 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM7A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121108,857,596 - 108,949,793 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl21108,854,477 - 108,949,735 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660725,511,802 - 5,601,682 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm7a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476520,376,684 - 20,449,026 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476520,370,492 - 20,448,969 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in KDM7A
586 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 2 6 5 6 7 7 1
Low 3 5 16 6 1 6 6 5 8 3 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000006395   ⟹   ENSCAFP00000005920
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl168,740,492 - 8,814,402 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000068554   ⟹   ENSCAFP00000047755
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl168,740,492 - 8,813,868 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845055235   ⟹   ENSCAFP00845043443
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl168,660,194 - 8,737,535 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845055236   ⟹   ENSCAFP00845043444
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl168,660,194 - 8,737,535 (+)Ensembl
RefSeq Acc Id: XM_038452805   ⟹   XP_038308733
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha169,583,276 - 9,664,675 (+)NCBI
RefSeq Acc Id: XM_038497070   ⟹   XP_038352998
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1168,610,970 - 8,692,356 (+)NCBI
RefSeq Acc Id: XM_038559409   ⟹   XP_038415337
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0168,524,015 - 8,605,439 (+)NCBI
RefSeq Acc Id: XM_038623389   ⟹   XP_038479317
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0168,455,403 - 8,536,816 (+)NCBI
RefSeq Acc Id: XM_038689108   ⟹   XP_038545036
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0168,660,254 - 8,741,637 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSCAFP00000005920   ⟸   ENSCAFT00000006395
RefSeq Acc Id: ENSCAFP00000047755   ⟸   ENSCAFT00000068554
RefSeq Acc Id: XP_038352998   ⟸   XM_038497070
RefSeq Acc Id: XP_038479317   ⟸   XM_038623389
RefSeq Acc Id: XP_038545036   ⟸   XM_038689108
- UniProtKB: A0A8C0MN35 (UniProtKB/TrEMBL),   A0A8I3QDR1 (UniProtKB/TrEMBL),   A0A8C0LDI0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038308733   ⟸   XM_038452805
- UniProtKB: A0A8C0MN35 (UniProtKB/TrEMBL),   A0A8I3QDR1 (UniProtKB/TrEMBL),   A0A8C0LDI0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038415337   ⟸   XM_038559409
- UniProtKB: A0A8C0LDI0 (UniProtKB/TrEMBL),   A0A8C0MN35 (UniProtKB/TrEMBL),   A0A8I3QDR1 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845043443   ⟸   ENSCAFT00845055235
RefSeq Acc Id: ENSCAFP00845043444   ⟸   ENSCAFT00845055236
Protein Domains
JmjC   PHD-type

Promoters
RGD ID:13686036
Promoter ID:EPDNEW_C4105
Type:single initiation site
Name:KDM7A_1
Description:lysine demethylase 7A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1168,740,579 - 8,740,639EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000003990 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030005814 UniProtKB/TrEMBL
  ENSCAFG00040007951 UniProtKB/TrEMBL
  ENSCAFG00845031073 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000006395.5 UniProtKB/TrEMBL
  ENSCAFT00000068554.2 UniProtKB/TrEMBL
  ENSCAFT00030010655.1 UniProtKB/TrEMBL
  ENSCAFT00030010756.1 UniProtKB/TrEMBL
  ENSCAFT00040014822.1 UniProtKB/TrEMBL
  ENSCAFT00040014884.1 UniProtKB/TrEMBL
  ENSCAFT00845055235 ENTREZGENE
  ENSCAFT00845055235.1 UniProtKB/TrEMBL
  ENSCAFT00845055236.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.1360 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  Cupin UniProtKB/TrEMBL
InterPro JHD UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene KDM7A ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE 7A UniProtKB/TrEMBL
  PHD/F-BOX CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam JHD UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
PROSITE JMJC UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
  SSF57903 UniProtKB/TrEMBL
UniProt A0A8C0LDI0 ENTREZGENE
  A0A8C0MFG6_CANLF UniProtKB/TrEMBL
  A0A8C0MN35 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0QPC0_CANLF UniProtKB/TrEMBL
  A0A8I3Q689_CANLF UniProtKB/TrEMBL
  A0A8I3QDR1 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:51806 ENTREZGENE