LOC102027630 (histone H4) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LOC102027630 (histone H4) Chinchilla lanigera
Analyze
Symbol: LOC102027630 (Ensembl: H4-16)
Name: histone H4
RGD ID: 8999253
Description: ENCODES a protein that exhibits structural constituent of chromatin (ortholog); INVOLVED IN negative regulation of megakaryocyte differentiation (ortholog); nucleosome assembly (ortholog); ASSOCIATED WITH autosomal dominant intellectual developmental disorder 6 (ortholog); genetic disease (ortholog); FOUND IN CENP-A containing nucleosome (ortholog); nucleosome (ortholog); nucleus (ortholog)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541311,517,245 - 11,517,556 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541311,517,229 - 11,517,609 (-)NCBIChiLan1.0ChiLan1.0
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
LOC102027630
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541311,517,245 - 11,517,556 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541311,517,229 - 11,517,609 (-)NCBIChiLan1.0ChiLan1.0
H4C16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381214,770,720 - 14,771,131 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1214,767,999 - 14,771,131 (-)EnsemblGRCh38hg38GRCh38
GRCh371214,923,654 - 14,924,065 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361214,814,921 - 14,815,332 (-)NCBINCBI36Build 36hg18NCBI36
Build 341214,814,920 - 14,815,332NCBI
Celera1220,068,629 - 20,069,040 (-)NCBICelera
Cytogenetic Map12p12.3NCBI
HuRef1214,692,924 - 14,693,335 (-)NCBIHuRef
CHM1_11214,889,747 - 14,890,158 (-)NCBICHM1_1
T2T-CHM13v2.01214,648,070 - 14,648,481 (-)NCBIT2T-CHM13v2.0
H4c16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396136,780,991 - 136,781,429 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6136,778,551 - 136,781,413 (-)EnsemblGRCm39 Ensembl
GRCm386136,803,993 - 136,804,431 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6136,801,553 - 136,804,415 (-)EnsemblGRCm38mm10GRCm38
MGSCv376136,752,589 - 136,752,900 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366136,768,264 - 136,768,575 (-)NCBIMGSCv36mm8
Celera6139,852,914 - 139,853,225 (-)NCBICelera
Cytogenetic Map6G1NCBI
cM Map666.72NCBI
LOC100976584
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21020,187,911 - 20,222,966 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11220,184,672 - 20,219,714 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01214,754,453 - 14,776,508 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11215,171,760 - 15,173,990 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1215,173,609 - 15,173,920 (-)Ensemblpanpan1.1panPan2
H4C16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12731,839,899 - 31,840,463 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2731,840,011 - 31,840,322 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2714,608,540 - 14,609,077 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02732,146,744 - 32,147,281 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2732,146,809 - 32,147,120 (+)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl3524,377,716 - 24,378,246 (-)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl3524,093,463 - 24,093,774 (+)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl3525,240,757 - 25,241,094 (-)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl3524,099,907 - 24,100,218 (-)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl3524,160,111 - 24,160,422 (+)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl3524,324,151 - 24,324,462 (+)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl3525,204,307 - 25,204,780 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12732,035,955 - 32,036,492 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02731,994,734 - 31,995,271 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02714,340,547 - 14,341,084 (-)NCBIUU_Cfam_GSD_1.0
LOC101978127
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494592,974,412 - 92,974,939 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365872,702,038 - 2,704,472 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
H4C20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1721,588,850 - 21,589,244 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HIST4H4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11114,668,897 - 14,670,947 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606920,639,558 - 20,641,276 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101719930
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475223,243,077 - 23,249,832 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475223,249,356 - 23,250,067 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000026236   ⟹   ENSCLAP00000025930
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495541311,517,245 - 11,517,556 (-)Ensembl
RefSeq Acc Id: XM_013511443   ⟹   XP_013366897
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495541311,517,229 - 11,517,609 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_013366897   ⟸   XM_013511443
- UniProtKB: A0A8C2W697 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCLAP00000025930   ⟸   ENSCLAT00000026236
Protein Domains
TATA box binding protein associated factor (TAF)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000003650 UniProtKB/TrEMBL
  ENSCLAG00000017446 UniProtKB/TrEMBL
  ENSCLAG00000017464 UniProtKB/TrEMBL
  ENSCLAG00000017472 UniProtKB/TrEMBL
  ENSCLAG00000017508 UniProtKB/TrEMBL
  ENSCLAG00000017552 UniProtKB/TrEMBL
  ENSCLAG00000017561 UniProtKB/TrEMBL
  ENSCLAG00000017582 UniProtKB/TrEMBL
  ENSCLAG00000018054 UniProtKB/TrEMBL
  ENSCLAG00000018062 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000005236.1 UniProtKB/TrEMBL
  ENSCLAT00000025620.1 UniProtKB/TrEMBL
  ENSCLAT00000025638.1 UniProtKB/TrEMBL
  ENSCLAT00000025646.1 UniProtKB/TrEMBL
  ENSCLAT00000025682.1 UniProtKB/TrEMBL
  ENSCLAT00000025726.1 UniProtKB/TrEMBL
  ENSCLAT00000025735.1 UniProtKB/TrEMBL
  ENSCLAT00000025756.1 UniProtKB/TrEMBL
  ENSCLAT00000026228.1 UniProtKB/TrEMBL
  ENSCLAT00000026236 ENTREZGENE
  ENSCLAT00000026236.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
InterPro CENP-T/H4_C UniProtKB/TrEMBL
  Histone-fold UniProtKB/TrEMBL
  Histone_H4 UniProtKB/TrEMBL
  Histone_H4_CS UniProtKB/TrEMBL
  TAF_TATA-bd_Histone-like_dom UniProtKB/TrEMBL
NCBI Gene LOC102027630 ENTREZGENE
PANTHER HISTONE H4 UniProtKB/TrEMBL
  HISTONE H4 UniProtKB/TrEMBL
Pfam CENP-T_C UniProtKB/TrEMBL
PRINTS HISTONEH4 UniProtKB/TrEMBL
PROSITE HISTONE_H4 UniProtKB/TrEMBL
SMART SM00417 UniProtKB/TrEMBL
  TAF UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/TrEMBL
UniProt A0A8C2W697 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-25 LOC102027630  histone H4    histone H4-like  Symbol and/or name change 5135510 APPROVED