Chaf1a (chromatin assembly factor 1 subunit A) - Rat Genome Database

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Gene: Chaf1a (chromatin assembly factor 1 subunit A) Rattus norvegicus
Analyze
Symbol: Chaf1a
Name: chromatin assembly factor 1 subunit A
RGD ID: 1590865
Description: Predicted to have chromo shadow domain binding activity and identical protein binding activity. Predicted to be involved in DNA replication-dependent nucleosome assembly. Predicted to localize to CAF-1 complex; chromatin; and nucleus. Human ortholog(s) of this gene implicated in colon cancer; high grade glioma; neuroblastoma; and systemic lupus erythematosus. Orthologous to human CHAF1A (chromatin assembly factor 1 subunit A); PARTICIPATES IN histone modification pathway; INTERACTS WITH 1-naphthyl isothiocyanate; amiodarone; amphetamine.
Type: protein-coding
RefSeq Status: MODEL
Also known as: chromatin assembly factor 1, subunit A (p150); LOC363333; similar to Chromatin assembly factor 1 subunit A (CAF-1 subunit A) (Chromatin assembly factor I p150 subunit) (CAF-I 150 kDa subunit) (CAF-Ip150)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29873,953 - 900,701 (+)NCBI
Rnor_6.0 Ensembl911,001,129 - 11,027,506 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0911,000,869 - 11,027,631 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.099,987,808 - 10,013,968 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,606,375 - 7,633,116 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-colchicine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
adenine  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
amphetamine  (EXP)
arecoline  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite ion  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
cadmium atom  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dichloroacetic acid  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
folic acid  (ISO)
furan  (EXP,ISO)
genistein  (ISO)
hexadecanoic acid  (ISO)
imiquimod  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
mitomycin C  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
PCB138  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8858152   PMID:14718166   PMID:15882967   PMID:16826239  


Genomics

Comparative Map Data
Chaf1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29873,953 - 900,701 (+)NCBI
Rnor_6.0 Ensembl911,001,129 - 11,027,506 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0911,000,869 - 11,027,631 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.099,987,808 - 10,013,968 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,606,375 - 7,633,116 (-)NCBICelera
Cytogenetic Map9q12NCBI
CHAF1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl194,402,640 - 4,445,018 (+)EnsemblGRCh38hg38GRCh38
GRCh38194,402,596 - 4,448,322 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37194,402,637 - 4,443,394 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,353,660 - 4,394,394 (+)NCBINCBI36hg18NCBI36
Build 34194,353,659 - 4,394,394NCBI
Celera194,340,887 - 4,381,635 (+)NCBI
Cytogenetic Map19p13.3NCBI
HuRef194,165,022 - 4,205,855 (+)NCBIHuRef
CHM1_1194,402,254 - 4,442,980 (+)NCBICHM1_1
Chaf1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,347,416 - 56,375,026 (+)NCBIGRCm39mm39
GRCm39 Ensembl1756,347,439 - 56,379,289 (+)Ensembl
GRCm381756,040,416 - 56,068,026 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,040,439 - 56,072,289 (+)EnsemblGRCm38mm10GRCm38
MGSCv371756,179,839 - 56,207,449 (+)NCBIGRCm37mm9NCBIm37
MGSCv361755,633,709 - 55,661,319 (+)NCBImm8
Celera1759,459,078 - 59,486,688 (+)NCBICelera
Cytogenetic Map17DNCBI
Chaf1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,468,202 - 4,499,171 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554954,467,317 - 4,499,419 (-)NCBIChiLan1.0ChiLan1.0
CHAF1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1194,375,398 - 4,409,339 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,375,379 - 4,409,339 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0193,425,182 - 3,461,646 (+)NCBIMhudiblu_PPA_v0panPan3
CHAF1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,248,286 - 55,276,425 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,248,288 - 55,276,900 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2054,976,526 - 55,004,596 (-)NCBI
ROS_Cfam_1.02055,906,936 - 55,935,483 (-)NCBI
UMICH_Zoey_3.12054,968,017 - 54,996,066 (-)NCBI
UNSW_CanFamBas_1.02055,448,917 - 55,476,971 (-)NCBI
UU_Cfam_GSD_1.02055,647,621 - 55,675,686 (-)NCBI
Chaf1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,269,886 - 215,292,910 (-)NCBI
SpeTri2.0NW_0049365882,536,141 - 2,564,897 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHAF1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,380,708 - 74,411,825 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1274,380,706 - 74,411,875 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2274,873,653 - 74,904,761 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHAF1A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,134,405 - 4,174,281 (+)NCBI
ChlSab1.1 Ensembl64,137,738 - 4,174,988 (+)Ensembl
Chaf1a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248285,266,676 - 5,302,061 (-)NCBI

Position Markers
RH141481  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29900,438 - 900,639 (-)MAPPER
Rnor_6.0911,000,887 - 11,001,087NCBIRnor6.0
Rnor_5.099,987,834 - 9,988,034UniSTSRnor5.0
Celera97,606,393 - 7,606,593UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9116520166Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9190783415555026Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)91086939115509311Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:123
Count of miRNA genes:95
Interacting mature miRNAs:102
Transcripts:ENSRNOT00000071107
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
Medium 2 26 29 22 16 22 57 20 35 1
Low 1 17 28 19 3 19 8 11 17 15 6 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071107   ⟹   ENSRNOP00000063994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl911,001,129 - 11,027,506 (-)Ensembl
RefSeq Acc Id: XM_001061702   ⟹   XP_001061702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera97,606,375 - 7,633,116 (-)NCBI
Sequence:
RefSeq Acc Id: XM_343671   ⟹   XP_343672
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29873,953 - 900,701 (+)NCBI
Rnor_6.0911,000,869 - 11,027,631 (-)NCBI
Rnor_5.099,987,808 - 10,013,968 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_343672 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83668 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001061702   ⟸   XM_001061702
- Sequence:
RefSeq Acc Id: XP_343672   ⟸   XM_343671
- UniProtKB: M0R3S3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063994   ⟸   ENSRNOT00000071107
Protein Domains
CAF1-p150_C2   CAF1-p150_N

Transcriptome

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

Promoters
RGD ID:13696477
Promoter ID:EPDNEW_R6996
Type:initiation region
Name:Chaf1a_1
Description:chromatin assembly factor 1 subunit A
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_6.0911,027,489 - 11,027,549EPDNEW

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)
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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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/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
SHRSP/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
SR/JrHsd (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: 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:1590865 AgrOrtholog
Ensembl Genes ENSRNOG00000046479 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063994 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071107 UniProtKB/TrEMBL
InterPro CAF1-p150_C2 UniProtKB/TrEMBL
  CAF1-p150_N UniProtKB/TrEMBL
  CAF1A UniProtKB/TrEMBL
KEGG Report rno:363333 UniProtKB/TrEMBL
NCBI Gene 363333 ENTREZGENE
Pfam CAF1-p150_C2 UniProtKB/TrEMBL
  CAF1-p150_N UniProtKB/TrEMBL
  CAF1A UniProtKB/TrEMBL
PhenoGen Chaf1a PhenoGen
UniProt M0R3S3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Chaf1a  chromatin assembly factor 1 subunit A  Chaf1a  chromatin assembly factor 1, subunit A (p150)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Chaf1a  chromatin assembly factor 1, subunit A (p150)  LOC363333  similar to Chromatin assembly factor 1 subunit A (CAF-1 subunit A) (Chromatin assembly factor I p150 subunit) (CAF-I 150 kDa subunit) (CAF-Ip150)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC363333  similar to Chromatin assembly factor 1 subunit A (CAF-1 subunit A) (Chromatin assembly factor I p150 subunit) (CAF-I 150 kDa subunit) (CAF-Ip150)      Symbol and Name status set to provisional 70820 PROVISIONAL