LOC100627380 (lysine-specific demethylase 4D-like) - Rat Genome Database

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Pathways
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Gene: LOC100627380 (lysine-specific demethylase 4D-like) Sus scrofa
Analyze
Symbol: LOC100627380
Name: lysine-specific demethylase 4D-like
RGD ID: 14268046
Description: ENCODES a protein that exhibits chromatin DNA binding (ortholog); damaged DNA binding (ortholog); histone demethylase activity (ortholog); INVOLVED IN cellular response to ionizing radiation (ortholog); DNA damage response (ortholog); double-strand break repair via homologous recombination (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH ataxia telangiectasia (ortholog); genetic disease (ortholog); intellectual disability (ortholog); FOUND IN pericentric heterochromatin (ortholog); site of double-strand break (ortholog)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1927,083,348 - 27,085,693 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2930,996,547 - 30,998,411 (+)NCBISscrofa10.2Sscrofa10.2susScr3
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

Cellular Component

Molecular Function

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


Genomics

Comparative Map Data
LOC100627380
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1927,083,348 - 27,085,693 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2930,996,547 - 30,998,411 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM4D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381194,973,709 - 94,999,519 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1194,973,709 - 94,999,519 (+)EnsemblGRCh38hg38GRCh38
GRCh371194,706,873 - 94,732,683 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361194,346,493 - 94,372,326 (+)NCBINCBI36Build 36hg18NCBI36
Build 341194,346,492 - 94,372,322NCBI
Celera1191,994,632 - 92,020,465 (+)NCBICelera
Cytogenetic Map11q21NCBI
HuRef1190,771,786 - 90,797,622 (+)NCBIHuRef
CHM1_11194,589,894 - 94,615,685 (+)NCBICHM1_1
T2T-CHM13v2.01194,980,727 - 95,006,531 (+)NCBIT2T-CHM13v2.0
Kdm4d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39914,373,844 - 14,411,818 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl914,373,844 - 14,411,778 (-)EnsemblGRCm39 Ensembl
GRCm38914,462,548 - 14,500,522 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl914,462,548 - 14,500,482 (-)EnsemblGRCm38mm10GRCm38
MGSCv37914,267,025 - 14,304,926 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36914,212,978 - 14,250,879 (-)NCBIMGSCv36mm8
Celera911,743,297 - 11,781,220 (-)NCBICelera
Cytogenetic Map9A1- A2NCBI
cM Map94.05NCBI
Kdm4d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8819,561,253 - 19,586,412 (-)NCBIGRCr8
mRatBN7.2811,279,756 - 11,304,920 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx815,271,854 - 15,297,256 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0813,569,605 - 13,595,007 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0811,558,890 - 11,584,068 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0812,968,192 - 12,993,651 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl813,511,805 - 13,513,337 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0813,454,239 - 13,456,523 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4811,222,556 - 11,247,715 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera812,774,633 - 12,798,709 (-)NCBICelera
Cytogenetic Map8q12NCBI
Kdm4d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049556058,977 - 10,539 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049556057,585 - 32,650 (-)NCBIChiLan1.0ChiLan1.0
KDM4D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2995,827,863 - 95,853,819 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11196,919,287 - 96,945,255 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01189,987,537 - 90,013,421 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11193,509,937 - 93,535,825 (+)NCBIpanpan1.1PanPan1.1panPan2
LOC485121
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1216,002,292 - 6,037,344 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl215,987,723 - 6,004,783 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,013,480 - 6,048,512 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0216,183,585 - 6,218,049 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1215,970,707 - 6,005,729 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0216,033,623 - 6,068,647 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0216,081,461 - 6,116,493 (-)NCBIUU_Cfam_GSD_1.0
LOC101967900
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494779,836,345 - 79,838,225 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493667453,200 - 73,042 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC103248265
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1186,190,515 - 86,215,061 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl186,212,761 - 86,214,490 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604339,576,496 - 39,600,714 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm4d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473539,640,090 - 39,695,833 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LOC100627380
130 total Variants

Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005667256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AEMK02000070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: XM_005667256   ⟹   XP_005667313
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1927,083,348 - 27,085,693 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005667313 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000038740.1
Reference Protein Sequences
RefSeq Acc Id: XP_005667313   ⟸   XM_005667256
- UniProtKB: A0A287A468 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
JmjC   JmjN


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000034794 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000066059.1 UniProtKB/TrEMBL
Gene3D-CATH Cupin UniProtKB/TrEMBL
InterPro JmjC_dom UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
NCBI Gene LOC100627380 ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 4D UniProtKB/TrEMBL
Pfam JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
PROSITE JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
UniProt A0A287A468 ENTREZGENE, UniProtKB/TrEMBL