Hist2h4a (histone cluster 2 H4 family member A) - Rat Genome Database

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Gene: Hist2h4a (histone cluster 2 H4 family member A) Rattus norvegicus
Analyze
Symbol: Hist2h4a
Name: histone cluster 2 H4 family member A
RGD ID: 1565073
Description: Predicted to enable protein domain specific binding activity. Predicted to be involved in DNA replication-dependent nucleosome assembly; DNA replication-independent nucleosome assembly; and negative regulation of megakaryocyte differentiation. Predicted to be located in nuclear chromosome. Predicted to be part of nucleosome. Orthologous to human H4C4 (H4 clustered histone 4); INTERACTS WITH ammonium chloride; 2,3',4,4',5-Pentachlorobiphenyl (ortholog); 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
Also known as: histone cluster 2, H4; histone H4; LOC502913; RGD1565073; similar to germinal histone H4 gene
RGD Orthologs
Human
Mouse
Bonobo
Squirrel
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Genome Annotation Status: not in current annotation release
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0 Ensembl1743,673,294 - 43,673,605 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,092,537 - 170,092,848 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,117,014 - 170,117,325 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,763,605 - 170,763,916 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,815,684 - 44,815,995 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,770,250 - 43,770,561 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,522,140 - 44,526,583 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,744,591 - 44,744,902 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,144,951 - 170,145,262 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl2198,411,955 - 198,412,350 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,821,225 - 43,821,536 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,617,247 - 43,617,558 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04170,800,539 - 170,800,979 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04235,057,800 - 235,058,211 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44173,852,389 - 173,852,700 (-)NCBIRGSC3.4rn4RGSC3.4
Celera4158,292,966 - 158,293,277 (-)NCBICelera
Cytogenetic Map4q43NCBI
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

References

Additional References at PubMed
PMID:14585971   PMID:14718166   PMID:18474616   PMID:20498094   PMID:21636898   PMID:22368283   PMID:24699735   PMID:25615412  


Genomics

Comparative Map Data
Hist2h4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0 Ensembl1743,673,294 - 43,673,605 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,092,537 - 170,092,848 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,117,014 - 170,117,325 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,763,605 - 170,763,916 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,815,684 - 44,815,995 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,770,250 - 43,770,561 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,522,140 - 44,526,583 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,744,591 - 44,744,902 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,144,951 - 170,145,262 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl2198,411,955 - 198,412,350 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,821,225 - 43,821,536 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,617,247 - 43,617,558 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04170,800,539 - 170,800,979 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04235,057,800 - 235,058,211 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44173,852,389 - 173,852,700 (-)NCBIRGSC3.4rn4RGSC3.4
Celera4158,292,966 - 158,293,277 (-)NCBICelera
Cytogenetic Map4q43NCBI
H4C4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl626,188,710 - 26,189,112 (-)EnsemblGRCh38hg38GRCh38
GRCh38626,188,710 - 26,189,112 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37626,188,938 - 26,189,340 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,296,917 - 26,297,283 (-)NCBINCBI36hg18NCBI36
Build 34626,296,916 - 26,297,283NCBI
Celera627,418,239 - 27,418,605 (-)NCBI
Cytogenetic Map6p22.2NCBI
HuRef626,131,943 - 26,132,309 (-)NCBIHuRef
CHM1_1626,191,140 - 26,191,506 (-)NCBICHM1_1
H4c12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391321,934,315 - 21,934,723 (-)NCBIGRCm39mm39
GRCm39 Ensembl1321,934,364 - 21,934,675 (-)Ensembl
GRCm381321,750,145 - 21,750,553 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1321,750,194 - 21,750,505 (-)EnsemblGRCm38mm10GRCm38
MGSCv371321,842,063 - 21,842,374 (-)NCBIGRCm37mm9NCBIm37
MGSCv361321,757,659 - 21,757,970 (-)NCBImm8
Celera1322,025,683 - 22,025,994 (-)NCBICelera
Cytogenetic Map13A3.1NCBI
LOC112440134
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1626,683,799 - 26,684,669 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0626,022,725 - 26,024,812 (-)NCBIMhudiblu_PPA_v0panPan3
LOC101972420
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049461,602,142 - 1,602,548 (+)NCBI
SpeTri2.0NW_0049366712,019,007 - 2,019,428 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC103222008
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11746,063,991 - 46,064,593 (+)NCBI
ChlSab1.1 Ensembl1114,670,283 - 14,670,591 (-)Ensembl
Vero_WHO_p1.0NW_02366604426,123,867 - 26,124,437 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478720Alc23Alcohol consumption QTL 230.00509drinking behavior trait (VT:0001422)ethanol drink intake rate to body weight ratio (CMO:0001616)4155386197184226339Rat
6478728Anxrr36Anxiety related response QTL 360.01061locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478733Anxrr37Anxiety related response QTL 370.00095locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478737Anxrr38Anxiety related response QTL 380.00159locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4145547014184226339Rat
6478757Anxrr44Anxiety related response QTL 440.01087locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
6478782Anxrr52Anxiety related response QTL 520.02091locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478785Anxrr53Anxiety related response QTL 530.01397locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4145547014184226339Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4145373934176509907Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157423126184226339Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4128602727173602727Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4156855449184226339Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4131864442176864442Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4131834282176834282Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4134917642179917642Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4146497452184226339Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:210
Count of miRNA genes:40
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000071690, ENSRNOT00000072147, ENSRNOT00000074198, ENSRNOT00000074356, ENSRNOT00000074526
Prediction methods: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.


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 33 46
Medium 3 40 100 41 55 41 38 41 44 53 61 50 38
Low 10 137 117 113 11 113 10 18 210 90 125 9 10
Below cutoff 1 37 24 24 24 3 80 24 18 3

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_578415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC097939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: XM_578415   ⟹   XP_578415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04170,800,539 - 170,800,979 (-)NCBI
Rnor_5.04235,057,800 - 235,058,211 (-)NCBI
RGSC_v3.44173,852,389 - 173,852,700 (-)RGD
Sequence:
Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565073 AgrOrtholog
Ensembl Genes ENSRNOG00000032224 Ensembl
  ENSRNOG00000045840 Ensembl
  ENSRNOG00000045978 Ensembl
  ENSRNOG00000046636 Ensembl
  ENSRNOG00000048215 Ensembl
  ENSRNOG00000048642 Ensembl
  ENSRNOG00000048735 Ensembl
  ENSRNOG00000050933 Ensembl
  ENSRNOG00000051891 Ensembl
  ENSRNOG00000054017 Ensembl
  ENSRNOG00000057690 Ensembl
  ENSRNOG00000058444 Ensembl
NCBI Gene 502913 ENTREZGENE
PhenoGen Hist2h4a PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-05-22 Hist2h4a  histone cluster 2 H4 family member A  Hist2h4a  histone cluster 2, H4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-07 Hist2h4a  histone cluster 2, H4  RGD1565073  similar to germinal histone H4 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1565073  similar to germinal histone H4 gene   RGD1565073_predicted  similar to germinal histone H4 gene (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565073_predicted  similar to germinal histone H4 gene (predicted)  LOC502913  similar to germinal histone H4 gene  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC502913  similar to germinal histone H4 gene      Symbol and Name status set to provisional 70820 PROVISIONAL