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 enable chromo shadow domain binding activity and identical protein binding activity. Predicted to be involved in DNA replication-dependent chromatin assembly and nucleosome assembly. Predicted to be part of CAF-1 complex and chromatin. Predicted to be active in 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; 17beta-estradiol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89961,225 - 987,825 (+)NCBIGRCr8
mRatBN7.29873,953 - 900,701 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9874,051 - 900,654 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0911,000,869 - 11,027,631 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl911,001,129 - 11,027,506 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,987,808 - 10,013,968 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,606,375 - 7,633,116 (-)NCBICelera
Cytogenetic Map9q11NCBI
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)
17beta-estradiol  (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)
6-propyl-2-thiouracil  (EXP)
adenine  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
amitrole  (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)
caffeine  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dextran sulfate  (ISO)
dichloroacetic acid  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
folic acid  (ISO)
FR900359  (ISO)
furan  (EXP,ISO)
genistein  (ISO)
gentamycin  (EXP)
hexadecanoic acid  (ISO)
imiquimod  (ISO)
maneb  (ISO)
methimazole  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
mitomycin C  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
niclosamide  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
PCB138  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
temozolomide  (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

References - curated
# Reference Title Reference Citation
1. Histone chaperone CHAF1A inhibits differentiation and promotes aggressive neuroblastoma. Barbieri E, etal., Cancer Res. 2014 Feb 1;74(3):765-74. doi: 10.1158/0008-5472.CAN-13-1315. Epub 2013 Dec 12.
2. Comprehensive analysis of the role of DNA repair gene polymorphisms on risk of glioma. Bethke L, etal., Hum Mol Genet. 2008 Mar 15;17(6):800-5. Epub 2007 Nov 29.
3. Histone chaperones in nucleosome assembly and human disease. Burgess RJ and Zhang Z, Nat Struct Mol Biol. 2013 Jan;20(1):14-22. doi: 10.1038/nsmb.2461.
4. Antibody against chromatin assembly factor-1 is a novel autoantibody specifically recognized in systemic lupus erythematosus. Doe K, etal., Lupus. 2014 Sep;23(10):1031-41. doi: 10.1177/0961203314536245. Epub 2014 May 16.
5. 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.
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Up-regulation of CHAF1A, a poor prognostic factor, facilitates cell proliferation of colon cancer. Wu Z, etal., Biochem Biophys Res Commun. 2014 Jun 27;449(2):208-15. doi: 10.1016/j.bbrc.2014.05.006. Epub 2014 May 15.
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
GRCr89961,225 - 987,825 (+)NCBIGRCr8
mRatBN7.29873,953 - 900,701 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9874,051 - 900,654 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0911,000,869 - 11,027,631 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl911,001,129 - 11,027,506 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,987,808 - 10,013,968 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,606,375 - 7,633,116 (-)NCBICelera
Cytogenetic Map9q11NCBI
CHAF1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38194,402,640 - 4,450,830 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl194,402,640 - 4,445,018 (+)EnsemblGRCh38hg38GRCh38
GRCh37194,402,637 - 4,443,394 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,353,660 - 4,394,394 (+)NCBINCBI36Build 36hg18NCBI36
Build 34194,353,659 - 4,394,394NCBI
Celera194,340,887 - 4,381,635 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef194,165,022 - 4,205,855 (+)NCBIHuRef
CHM1_1194,402,254 - 4,442,980 (+)NCBICHM1_1
T2T-CHM13v2.0194,386,080 - 4,434,290 (+)NCBIT2T-CHM13v2.0
Chaf1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,347,404 - 56,375,027 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,347,439 - 56,379,289 (+)EnsemblGRCm39 Ensembl
GRCm381756,040,416 - 56,068,026 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,040,439 - 56,072,289 (+)EnsemblGRCm38mm10GRCm38
MGSCv371756,179,839 - 56,207,449 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361755,633,709 - 55,661,319 (+)NCBIMGSCv36mm8
Celera1759,459,078 - 59,486,688 (+)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.13NCBI
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
NHGRI_mPanPan1-v2208,800,163 - 8,836,734 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1198,029,295 - 8,065,850 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,425,182 - 3,461,646 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1194,375,398 - 4,409,339 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,375,379 - 4,409,339 (+)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02055,906,936 - 55,935,483 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2055,907,073 - 55,935,515 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12054,968,017 - 54,996,066 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02055,448,917 - 55,476,971 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,647,621 - 55,675,686 (-)NCBIUU_Cfam_GSD_1.0
Chaf1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,269,886 - 215,292,910 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,542,265 - 2,564,962 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,536,141 - 2,564,897 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHAF1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,380,709 - 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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,134,405 - 4,174,281 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl64,137,738 - 4,174,988 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660814,024,455 - 4,068,581 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chaf1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248285,266,932 - 5,302,067 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248285,266,676 - 5,302,061 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chaf1a
25 total Variants
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.


QTLs in Region (mRatBN7.2)
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)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat

Markers in Region
RH141481  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29900,438 - 900,639 (-)MAPPERmRatBN7.2
Rnor_6.0911,000,887 - 11,001,087NCBIRnor6.0
Rnor_5.099,987,834 - 9,988,034UniSTSRnor5.0
Celera97,606,393 - 7,606,593UniSTS


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


RefSeq Acc Id: ENSRNOT00000071107   ⟹   ENSRNOP00000063994
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9874,051 - 900,654 (+)Ensembl
Rnor_6.0 Ensembl911,001,129 - 11,027,506 (-)Ensembl
RefSeq Acc Id: NM_001427323   ⟹   NP_001414252
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89961,225 - 987,825 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414252 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83668 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000063994.2
RefSeq Acc Id: ENSRNOP00000063994   ⟸   ENSRNOT00000071107
RefSeq Acc Id: NP_001414252   ⟸   NM_001427323
- UniProtKB: M0R3S3 (UniProtKB/TrEMBL)
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R3S3-F1-model_v2 AlphaFold M0R3S3 1-907 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590865 AgrOrtholog
BioCyc Gene G2FUF-28566 BioCyc
Ensembl Genes ENSRNOG00000046479 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071107.3 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
PANTHER CHROMATIN ASSEMBLY FACTOR 1 SUBUNIT A UniProtKB/TrEMBL
  CHROMATIN ASSEMBLY FACTOR 1 SUBUNIT A CAF-1 SUBUNIT A UniProtKB/TrEMBL
Pfam CAF-1_p150 UniProtKB/TrEMBL
  CAF1-p150_C2 UniProtKB/TrEMBL
  CAF1-p150_N UniProtKB/TrEMBL
  CAF1A UniProtKB/TrEMBL
PhenoGen Chaf1a PhenoGen
RatGTEx ENSRNOG00000046479 RatGTEx
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