H3c1 (H3 clustered histone 1) - Rat Genome Database

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Gene: H3c1 (H3 clustered histone 1) Rattus norvegicus
Analyze
Symbol: H3c1
Name: H3 clustered histone 1
RGD ID: 1598076
Description: Predicted to enable DNA binding activity and protein heterodimerization activity. Predicted to be a structural constituent of chromatin. Predicted to be involved in DNA replication-dependent chromatin assembly; epigenetic regulation of gene expression; and nucleosome assembly. Predicted to be located in nuclear chromosome. Predicted to be part of nucleosome. Orthologous to several human genes including H3C1 (H3 clustered histone 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; Cuprizon.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Hist1h3a; histone cluster 1 H3 family member A; histone cluster 1, H3a; histone cluster 3, H3; histone H3.1; LOC679994; similar to histone 1, H2ai
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21741,367,824 - 41,368,902 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1741,368,386 - 41,368,856 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01743,616,206 - 43,616,735 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,839,721 - 44,840,131 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,616,247 - 43,616,657 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,763,598 - 44,764,008 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,814,773 - 43,815,183 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01745,470,585 - 45,488,848 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41748,524,533 - 48,525,029 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1740,999,836 - 41,000,365 (+)NCBICelera
Cytogenetic Map17p11NCBI
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. 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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14718166   PMID:16267050   PMID:19135898   PMID:19946888   PMID:20458337   PMID:20498094   PMID:21630459   PMID:21636898   PMID:22720776   PMID:23376485   PMID:24699735   PMID:25468996  
PMID:25615412  


Genomics

Comparative Map Data
H3c1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21741,367,824 - 41,368,902 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1741,368,386 - 41,368,856 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01743,616,206 - 43,616,735 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,839,721 - 44,840,131 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,616,247 - 43,616,657 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,763,598 - 44,764,008 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,814,773 - 43,815,183 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01745,470,585 - 45,488,848 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41748,524,533 - 48,525,029 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1740,999,836 - 41,000,365 (+)NCBICelera
Cytogenetic Map17p11NCBI
H3C1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38626,020,451 - 26,020,958 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl626,020,451 - 26,020,958 (+)EnsemblGRCh38hg38GRCh38
GRCh37626,020,679 - 26,021,186 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,128,697 - 26,129,165 (+)NCBINCBI36Build 36hg18NCBI36
Build 34626,128,696 - 26,129,165NCBI
Celera627,247,942 - 27,248,410 (+)NCBICelera
Cytogenetic Map6p22.2NCBI
HuRef625,963,784 - 25,964,252 (+)NCBIHuRef
CHM1_1626,022,991 - 26,023,459 (+)NCBICHM1_1
T2T-CHM13v2.0625,886,390 - 25,886,897 (+)NCBIT2T-CHM13v2.0
H3c1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,945,868 - 23,946,369 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1323,945,836 - 23,946,369 (-)EnsemblGRCm39 Ensembl
GRCm381323,761,885 - 23,762,386 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,761,853 - 23,762,386 (-)EnsemblGRCm38mm10GRCm38
MGSCv371323,853,722 - 23,854,255 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361323,769,318 - 23,769,851 (-)NCBIMGSCv36mm8
Celera1323,993,618 - 23,994,151 (-)NCBICelera
Cytogenetic Map13A3.1NCBI

Position Markers
RH131033  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21741,386,153 - 41,386,335 (+)MAPPERmRatBN7.2
Rnor_6.01743,633,986 - 43,634,167NCBIRnor6.0
Rnor_5.01745,488,371 - 45,488,552UniSTSRnor5.0
RGSC_v3.41748,505,856 - 48,506,037UniSTSRGSC3.4
Celera1741,017,326 - 41,017,507UniSTS
Cytogenetic Map17p11UniSTS
UniSTS:488581  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21741,385,842 - 41,386,253 (+)MAPPERmRatBN7.2
Rnor_6.01743,633,675 - 43,634,085NCBIRnor6.0
Rnor_5.01745,488,060 - 45,488,470UniSTSRnor5.0
RGSC_v3.41748,505,938 - 48,506,348UniSTSRGSC3.4
Celera1741,017,015 - 41,017,425UniSTS
Cytogenetic Map17p11UniSTS
UniSTS:491901  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21741,369,321 - 41,369,768 (+)MAPPERmRatBN7.2
Rnor_6.01743,617,155 - 43,617,601NCBIRnor6.0
Rnor_5.01745,471,540 - 45,471,986UniSTSRnor5.0
RGSC_v3.41748,523,669 - 48,524,115UniSTSRGSC3.4
Celera1741,000,785 - 41,001,231UniSTS
Cytogenetic Map17p11UniSTS
UniSTS:493012  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21741,368,413 - 41,368,824 (+)MAPPERmRatBN7.2
Rnor_6.01743,616,247 - 43,616,657NCBIRnor6.0
Rnor_5.01745,470,632 - 45,471,042UniSTSRnor5.0
RGSC_v3.41748,524,613 - 48,525,023UniSTSRGSC3.4
Celera1740,999,877 - 41,000,287UniSTS
Cytogenetic Map17p11UniSTS


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


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000094137   ⟹   ENSRNOP00000080297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1741,368,386 - 41,368,856 (+)Ensembl
RefSeq Acc Id: XM_017600720   ⟹   XP_017456209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21741,367,824 - 41,368,902 (+)NCBI
Rnor_6.01743,616,206 - 43,616,735 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001395691 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456209 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_017456209   ⟸   XM_017600720
- UniProtKB: Q6LED0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000080297   ⟸   ENSRNOT00000094137

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6LED0-F1-model_v2 AlphaFold Q6LED0 1-136 view protein structure

Transcriptome

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

Promoters
RGD ID:13700456
Promoter ID:EPDNEW_R10977
Type:multiple initiation site
Name:Hist1h2ail1_1
Description:histone cluster 1 H2a family member I like 1
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_6.01743,616,212 - 43,616,272EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 43616305 43616306 A G snv WN/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1598076 AgrOrtholog
BioCyc Gene G2FUF-9386 BioCyc
Ensembl Genes ENSRNOG00000046144 Ensembl
  ENSRNOG00000046434 Ensembl
  ENSRNOG00000054539 Ensembl
  ENSRNOG00000056281 Ensembl
  ENSRNOG00000063167 UniProtKB/Swiss-Prot
  ENSRNOG00000064755 UniProtKB/Swiss-Prot
  ENSRNOG00000068516 UniProtKB/Swiss-Prot
  ENSRNOG00000068614 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000080297 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000091493 UniProtKB/Swiss-Prot
  ENSRNOP00000095460 UniProtKB/Swiss-Prot
  ENSRNOP00000096532 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000094137 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000095973 UniProtKB/Swiss-Prot
  ENSRNOT00000101837 UniProtKB/Swiss-Prot
  ENSRNOT00000117255 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot
InterPro Histone-fold UniProtKB/Swiss-Prot
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot
  Histone_H3/CENP-A UniProtKB/Swiss-Prot
KEGG Report rno:291159 UniProtKB/Swiss-Prot
  rno:679994 UniProtKB/Swiss-Prot
NCBI Gene 679994 ENTREZGENE
PANTHER PTHR11426 UniProtKB/Swiss-Prot
Pfam Histone UniProtKB/Swiss-Prot
PhenoGen H3c1 PhenoGen
PRINTS HISTONEH3 UniProtKB/Swiss-Prot
PROSITE HISTONE_H3_1 UniProtKB/Swiss-Prot
  HISTONE_H3_2 UniProtKB/Swiss-Prot
SMART SM00428 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot
UniProt H31_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 H3c1  H3 clustered histone 1  H3c1  H3 clustered histone 1  Data Merged 737654 PROVISIONAL
2021-08-09 H3c1  H3 clustered histone 1      Symbol and Name status set to provisional 45752 PROVISIONAL
2019-09-11 H3c1  H3 clustered histone 1  Hist1h3a  histone cluster 1 H3 family member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-05-24 Hist1h3a  histone cluster 1 H3 family member A  Hist1h3a  histone cluster 1, H3a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-09 Hist1h3a  histone cluster 1, H3a  LOC679994  similar to histone 1, H2ai  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-28 LOC679994  similar to histone 1, H2ai   LOC679994  similar to histone 1, H2ai (predicted)  'predicted' is removed from gene name 2292626 APPROVED
2006-11-20 LOC679994  similar to histone 1, H2ai (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL