Kdm4b (lysine demethylase 4B) - Rat Genome Database

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Gene: Kdm4b (lysine demethylase 4B) Heterocephalus glaber
Analyze
Symbol: Kdm4b
Name: lysine demethylase 4B
RGD ID: 18916284
Description: ENCODES a protein that exhibits histone demethylase activity (ortholog); histone H3K36 demethylase activity (ortholog); INVOLVED IN brain development (ortholog); chromatin remodeling (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH alopecia areata (ortholog); Autosomal Dominant Intellectual Developmental Disorder 65 (ortholog); breast cancer (ortholog); FOUND IN cytosol (ortholog); nucleoplasm (ortholog); pericentric heterochromatin (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Lysine-specific demethylase 4B
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248284,796,972 - 4,864,638 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248284,796,306 - 4,893,093 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:21993625   PMID:30032202  


Genomics

Comparative Map Data
Kdm4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248284,796,972 - 4,864,638 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248284,796,306 - 4,893,093 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
KDM4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38194,969,113 - 5,153,598 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl194,969,113 - 5,153,598 (+)EnsemblGRCh38hg38GRCh38
GRCh37194,969,124 - 5,153,609 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,920,132 - 5,104,606 (+)NCBINCBI36Build 36hg18NCBI36
Celera194,906,316 - 5,091,160 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef194,730,929 - 4,915,533 (+)NCBIHuRef
CHM1_1194,969,172 - 5,153,207 (+)NCBICHM1_1
T2T-CHM13v2.0194,954,509 - 5,140,176 (+)NCBIT2T-CHM13v2.0
Kdm4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,632,975 - 56,710,774 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,633,062 - 56,709,870 (+)EnsemblGRCm39 Ensembl
GRCm381756,325,970 - 56,403,774 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,326,062 - 56,402,870 (+)EnsemblGRCm38mm10GRCm38
MGSCv371756,465,473 - 56,542,296 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361755,959,801 - 56,036,572 (+)NCBIMGSCv36mm8
Celera1760,697,409 - 60,748,612 (+)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.27NCBI
Kdm4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,245,885 - 1,324,384 (+)NCBIGRCr8
mRatBN7.291,158,737 - 1,237,233 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,158,752 - 1,236,543 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,604,418 - 1,682,893 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,952,414 - 7,030,893 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,909,462 - 5,987,943 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,656,035 - 10,734,127 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,653,216 - 10,734,073 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,647,087 - 9,725,878 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,273,613 - 7,351,363 (-)NCBICelera
Cytogenetic Map9q11NCBI
Kdm4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,018,770 - 4,114,604 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554954,019,066 - 4,101,577 (-)NCBIChiLan1.0ChiLan1.0
KDM4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2209,362,473 - 9,551,249 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1198,591,717 - 8,777,748 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,986,296 - 4,172,359 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1194,977,413 - 5,116,113 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,977,413 - 5,116,113 (+)Ensemblpanpan1.1panPan2
KDM4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12054,713,900 - 54,843,991 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2054,634,121 - 54,820,816 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2054,438,687 - 54,576,517 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02055,368,796 - 55,506,632 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2055,370,326 - 55,506,729 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12054,430,228 - 54,567,939 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02054,910,865 - 55,048,624 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,108,670 - 55,246,485 (-)NCBIUU_Cfam_GSD_1.0
Kdm4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,829,153 - 214,917,129 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,908,899 - 3,005,674 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,908,970 - 3,005,625 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl273,747,669 - 73,889,866 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1273,746,379 - 73,889,881 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2274,436,488 - 74,458,404 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,649,140 - 4,831,634 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl64,649,221 - 4,831,636 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660813,296,265 - 3,480,930 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSHGLT00000019429   ⟹   ENSHGLP00000019238
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046248284,796,972 - 4,864,638 (-)Ensembl
RefSeq Acc Id: ENSHGLT00000019430   ⟹   ENSHGLP00000019239
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046248284,796,972 - 4,864,638 (-)Ensembl
RefSeq Acc Id: XM_004865707   ⟹   XP_004865764
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248284,796,306 - 4,893,093 (-)NCBI
RefSeq Acc Id: XM_004865709   ⟹   XP_004865766
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248284,796,306 - 4,893,093 (-)NCBI
RefSeq Acc Id: XM_021244801   ⟹   XP_021100460
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248284,800,782 - 4,893,093 (-)NCBI
RefSeq Acc Id: XM_021244802   ⟹   XP_021100461
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248284,850,221 - 4,893,093 (-)NCBI
Protein Sequences
Protein RefSeqs XP_004865764 (Get FASTA)   NCBI Sequence Viewer  
  XP_004865766 (Get FASTA)   NCBI Sequence Viewer  
  XP_021100460 (Get FASTA)   NCBI Sequence Viewer  
  XP_021100461 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EHB15122 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000019238
Reference Protein Sequences
RefSeq Acc Id: XP_004865766   ⟸   XM_004865709
- Peptide Label: isoform X2
- UniProtKB: G5C0R1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004865764   ⟸   XM_004865707
- Peptide Label: isoform X1
- UniProtKB: G5C0R1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_021100460   ⟸   XM_021244801
- Peptide Label: isoform X3
RefSeq Acc Id: XP_021100461   ⟸   XM_021244802
- Peptide Label: isoform X4
RefSeq Acc Id: ENSHGLP00000019238   ⟸   ENSHGLT00000019429
RefSeq Acc Id: ENSHGLP00000019239   ⟸   ENSHGLT00000019430


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000013802 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000019429 ENTREZGENE
Gene3D-CATH 2.30.30.140 UniProtKB/TrEMBL
  3.10.330.70 UniProtKB/TrEMBL
  Cupin UniProtKB/TrEMBL
  Zinc/RING finger domain, C3HC4 (zinc finger) UniProtKB/TrEMBL
InterPro EPHD UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  KDM4-like_Tudor UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
  Tudor_KDM4B_rpt1 UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene Kdm4b ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 4B UniProtKB/TrEMBL
Pfam JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD_2 UniProtKB/TrEMBL
  Tudor_2 UniProtKB/TrEMBL
  zf-HC5HC2H_2 UniProtKB/TrEMBL
PROSITE EPHD UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  TUDOR UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
  FYVE/PHD zinc finger UniProtKB/TrEMBL
  Tudor/PWWP/MBT UniProtKB/TrEMBL
UniProt G5C0R1 ENTREZGENE, UniProtKB/TrEMBL