H4f3 (H1.3 linker histone, cluster member) - Rat Genome Database

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Gene: H4f3 (H1.3 linker histone, cluster member) Rattus norvegicus
Analyze
Symbol: H4f3
Name: H1.3 linker histone, cluster member
RGD ID: 1585568
Description: Predicted to enable double-stranded DNA binding activity and nucleosomal DNA binding activity. Predicted to be a structural constituent of chromatin. Predicted to be involved in chromosome condensation and negative regulation of DNA recombination. Predicted to act upstream of or within chromatin organization; histone lysine methylation; and negative regulation of transcription by RNA polymerase II. Predicted to be located in euchromatin. Predicted to be part of nucleosome. Predicted to be active in nucleus. Orthologous to human H1-3 (H1.3 linker histone, cluster member); INTERACTS WITH aconitine; gentamycin; paracetamol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Hist1h1d; histone cluster 1 H1 family member d; histone H1.3; LOC684828; similar to Histone H1.2 (H1 VAR.1) (H1c); uncharacterized protein LOC684828
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21741,528,576 - 41,554,586 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1741,529,667 - 41,552,334 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01743,797,711 - 43,798,450 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,797,721 - 43,798,383 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01745,652,308 - 45,655,450 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1741,182,415 - 41,183,154 (-)NCBICelera
Cytogenetic Map17p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (ISO)
euchromatin  (ISO)
nucleosome  (IEA)
nucleus  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12808097   PMID:15562002   PMID:15911621   PMID:19882353   PMID:22083958   PMID:22681889   PMID:22701719  


Genomics

Comparative Map Data
H4f3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21741,528,576 - 41,554,586 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1741,529,667 - 41,552,334 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01743,797,711 - 43,798,450 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,797,721 - 43,798,383 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01745,652,308 - 45,655,450 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1741,182,415 - 41,183,154 (-)NCBICelera
Cytogenetic Map17p11NCBI
H1-3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38626,234,212 - 26,234,987 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl626,234,212 - 26,234,987 (-)EnsemblGRCh38hg38GRCh38
GRCh37626,234,440 - 26,235,215 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,342,419 - 26,343,195 (-)NCBINCBI36Build 36hg18NCBI36
Build 34626,342,418 - 26,343,195NCBI
Celera627,463,747 - 27,464,523 (-)NCBICelera
Cytogenetic Map6p22.2NCBI
HuRef626,177,448 - 26,178,221 (-)NCBIHuRef
CHM1_1626,236,600 - 26,237,376 (-)NCBICHM1_1
T2T-CHM13v2.0626,102,677 - 26,103,452 (-)NCBIT2T-CHM13v2.0
H1f3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,739,206 - 23,739,981 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1323,737,436 - 23,744,860 (+)EnsemblGRCm39 Ensembl
GRCm381323,555,032 - 23,555,807 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,553,262 - 23,560,686 (+)EnsemblGRCm38mm10GRCm38
MGSCv371323,646,901 - 23,649,877 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361323,562,499 - 23,565,473 (+)NCBIMGSCv36mm8
Celera1323,786,995 - 23,789,971 (+)NCBICelera
Cytogenetic Map13A3.1NCBI
H1-3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1626,729,188 - 26,729,978 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl626,729,239 - 26,729,904 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0626,068,439 - 26,071,115 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
H1-3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13524,155,864 - 24,156,647 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3524,007,247 - 24,010,246 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03524,334,721 - 24,338,937 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3524,338,211 - 24,338,867 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13524,115,793 - 24,118,793 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03524,167,683 - 24,171,900 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03525,632,339 - 25,636,554 (-)NCBIUU_Cfam_GSD_1.0
H1-3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1720,881,642 - 20,882,307 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2722,072,582 - 22,075,157 (+)NCBISscrofa10.2Sscrofa10.2susScr3
H1-3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11746,016,618 - 46,017,989 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1746,016,693 - 46,017,355 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604426,170,886 - 26,171,676 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in H4f3
94 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:120
Count of miRNA genes:102
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000075069
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318457246843Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172702794956836890Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172702794960463643Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172738994653481766Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173136839162109574Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173199078450909196Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173583708569599340Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
631497Bp98Blood pressure QTL 983.66arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)174135465160463643Rat

Markers in Region
Hist1h1d  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21741,551,589 - 41,552,232 (+)MAPPERmRatBN7.2
Rnor_6.01743,797,702 - 43,798,344NCBIRnor6.0
Rnor_5.01745,654,718 - 45,655,360UniSTSRnor5.0
Celera1741,182,406 - 41,183,048UniSTS


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 renal system reproductive system respiratory system appendage
High 6 9
Medium 8 18 8 7 8 8 8 8 8 8 8 8
Low 3 35 31 31 3 31 3 51 27 28 3
Below cutoff 2 2 2 13 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075069   ⟹   ENSRNOP00000065338
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1741,529,667 - 41,552,334 (-)Ensembl
Rnor_6.0 Ensembl1743,797,721 - 43,798,383 (-)Ensembl
RefSeq Acc Id: XM_039096140   ⟹   XP_038952068
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21741,536,648 - 41,554,586 (-)NCBI
RefSeq Acc Id: XM_039096141   ⟹   XP_038952069
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21741,528,576 - 41,554,586 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001395537 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952068 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952069 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL86589 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000065338   ⟸   ENSRNOT00000075069
RefSeq Acc Id: XP_038952069   ⟸   XM_039096141
- UniProtKB: M0R7B4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952068   ⟸   XM_039096140
- UniProtKB: M0R7B4 (UniProtKB/TrEMBL)
Protein Domains
H15

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R7B4-F1-model_v2 AlphaFold M0R7B4 1-220 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700471
Promoter ID:EPDNEW_R10991
Type:single initiation site
Name:Hist1h1d_1
Description:histone cluster 1 H1 family member d
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01743,798,433 - 43,798,493EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1585568 AgrOrtholog
BioCyc Gene G2FUF-9370 BioCyc
Ensembl Genes ENSRNOG00000048264 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065338 ENTREZGENE
  ENSRNOP00000065338.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075069 ENTREZGENE
  ENSRNOT00000075069.3 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro Histone_H1/H5 UniProtKB/TrEMBL
  Histone_H5 UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene 684828 ENTREZGENE
Pfam Linker_histone UniProtKB/TrEMBL
PhenoGen H4f3 PhenoGen
PRINTS HISTONEH5 UniProtKB/TrEMBL
PROSITE H15 UniProtKB/TrEMBL
SMART H15 UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt M0R7B4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-09-13 H4f3  H1.3 linker histone, cluster member  Hist1h1d  histone cluster 1 H1 family member d  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-05-23 Hist1h1d  histone cluster 1 H1 family member d  LOC684828  similar to Histone H1.2 (H1 VAR.1) (H1c)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC684828  similar to Histone H1.2 (H1 VAR.1) (H1c)      Symbol and Name status set to provisional 70820 PROVISIONAL