Asf1a (anti-silencing function 1A histone chaperone) - Rat Genome Database

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Gene: Asf1a (anti-silencing function 1A histone chaperone) Rattus norvegicus
Analyze
Symbol: Asf1a
Name: anti-silencing function 1A histone chaperone
RGD ID: 1311941
Description: Predicted to enable chromatin binding activity; histone binding activity; and histone chaperone activity. Predicted to be involved in DNA replication-dependent chromatin assembly. Predicted to act upstream of or within several processes, including DNA repair; nucleosome assembly; and osteoblast differentiation. Predicted to be located in chromatin and nucleoplasm. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Orthologous to human ASF1A (anti-silencing function 1A histone chaperone); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: ASF1 anti-silencing function 1 homolog A; ASF1 anti-silencing function 1 homolog A (S. cerevisiae); histone chaperone ASF1A; LOC294408
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
mRatBN7.22032,893,962 - 32,908,808 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2032,893,573 - 32,908,808 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2033,933,507 - 33,948,491 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02033,324,220 - 33,339,204 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02034,051,143 - 34,066,130 (+)NCBIRnor_WKY
Rnor_6.02034,894,419 - 34,909,265 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2034,894,419 - 34,909,265 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02036,651,864 - 36,666,710 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42032,261,624 - 32,276,470 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12032,242,606 - 32,288,661 (+)NCBI
Celera2034,286,255 - 34,301,101 (+)NCBICelera
Cytogenetic Map20q11NCBI
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
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3-methyl-3H-imidazo[4,5-f]quinolin-2-amine  (ISO)
4-nitro-1,2-phenylenediamine  (ISO)
aflatoxin B1  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
chlorambucil  (ISO)
chromium(6+)  (ISO)
clofibrate  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Ethyl acrylate  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
menadione  (ISO)
mercury dibromide  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
N-nitrosodimethylamine  (ISO)
nefazodone  (EXP)
oxaliplatin  (EXP)
p-chloromercuribenzoic acid  (ISO)
para-Cresidine  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
rac-lactic acid  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
thimerosal  (ISO)
topotecan  (EXP)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
zinc protoporphyrin  (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 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.
2. 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.
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10759893   PMID:11897662   PMID:14718166   PMID:21493898   PMID:22705305   PMID:24105743  


Genomics

Comparative Map Data
Asf1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22032,893,962 - 32,908,808 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2032,893,573 - 32,908,808 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2033,933,507 - 33,948,491 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02033,324,220 - 33,339,204 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02034,051,143 - 34,066,130 (+)NCBIRnor_WKY
Rnor_6.02034,894,419 - 34,909,265 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2034,894,419 - 34,909,265 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02036,651,864 - 36,666,710 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42032,261,624 - 32,276,470 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12032,242,606 - 32,288,661 (+)NCBI
Celera2034,286,255 - 34,301,101 (+)NCBICelera
Cytogenetic Map20q11NCBI
ASF1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386118,894,152 - 118,909,171 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6118,894,152 - 118,909,171 (+)EnsemblGRCh38hg38GRCh38
GRCh376119,215,316 - 119,230,336 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366119,263,628 - 119,272,035 (+)NCBINCBI36Build 36hg18NCBI36
Build 346119,263,627 - 119,272,029NCBI
Celera6119,959,803 - 119,974,994 (+)NCBICelera
Cytogenetic Map6q22.31NCBI
HuRef6116,797,372 - 116,812,467 (+)NCBIHuRef
CHM1_16119,479,284 - 119,494,377 (+)NCBICHM1_1
T2T-CHM13v2.06120,079,995 - 120,095,013 (+)NCBIT2T-CHM13v2.0
Asf1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391053,473,057 - 53,485,321 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1053,472,853 - 53,485,321 (+)EnsemblGRCm39 Ensembl
GRCm381053,596,961 - 53,609,225 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1053,596,757 - 53,609,225 (+)EnsemblGRCm38mm10GRCm38
MGSCv371053,316,767 - 53,329,031 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361053,285,376 - 53,297,640 (+)NCBIMGSCv36mm8
Celera1054,424,436 - 54,436,700 (+)NCBICelera
Cytogenetic Map10B3NCBI
Asf1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554361,635,399 - 1,645,075 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554361,635,397 - 1,640,989 (+)NCBIChiLan1.0ChiLan1.0
ASF1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16120,843,523 - 120,858,477 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6120,843,461 - 120,858,471 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06116,702,314 - 116,717,445 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ASF1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1158,821,324 - 58,834,935 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl158,821,521 - 58,946,475 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha159,624,039 - 59,637,812 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0159,005,923 - 59,019,731 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl159,006,146 - 59,024,788 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1158,906,233 - 58,920,041 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0158,747,902 - 58,761,670 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0159,379,406 - 59,393,234 (+)NCBIUU_Cfam_GSD_1.0
Asf1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946109,592,255 - 109,606,875 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366581,699,044 - 1,715,582 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049366581,699,150 - 1,713,079 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ASF1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl143,200,415 - 43,214,913 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1143,200,339 - 43,215,019 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2148,350,741 - 48,365,279 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ASF1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11354,972,514 - 54,988,436 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1354,969,299 - 54,988,558 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604027,296,097 - 27,311,554 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Asf1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479811,306,849 - 11,317,075 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Asf1a
135 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:524
Count of miRNA genes:252
Interacting mature miRNAs:312
Transcripts:ENSRNOT00000000471
Prediction methods:Microtar, Miranda, 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
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203161428444396023Rat


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 30 39 23 19 23 5 5 74 32 39 11 5
Low 1 13 18 18 18 3 6 3 2 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000471   ⟹   ENSRNOP00000000471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2032,893,573 - 32,908,808 (+)Ensembl
Rnor_6.0 Ensembl2034,894,419 - 34,909,265 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084420   ⟹   ENSRNOP00000068723
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2034,895,059 - 34,907,451 (+)Ensembl
RefSeq Acc Id: NM_001106389   ⟹   NP_001099859
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22032,893,962 - 32,908,808 (+)NCBI
Rnor_6.02034,894,419 - 34,909,265 (+)NCBI
Rnor_5.02036,651,864 - 36,666,710 (+)NCBI
RGSC_v3.42032,261,624 - 32,276,470 (+)RGD
Celera2034,286,255 - 34,301,101 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099859 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92925 (Get FASTA)   NCBI Sequence Viewer  
  EDL92926 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099859   ⟸   NM_001106389
- UniProtKB: D3ZFM1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068723   ⟸   ENSRNOT00000084420
RefSeq Acc Id: ENSRNOP00000000471   ⟸   ENSRNOT00000000471

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZFM1-F1-model_v2 AlphaFold D3ZFM1 1-204 view protein structure

Transcriptome

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

Promoters
RGD ID:13701629
Promoter ID:EPDNEW_R12153
Type:single initiation site
Name:Asf1a_1
Description:anti-silencing function 1A histone chaperone
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_6.02034,894,364 - 34,894,424EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311941 AgrOrtholog
BioCyc Gene G2FUF-3625 BioCyc
Ensembl Genes ENSRNOG00000000415 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000471.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000471.7 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.1490 UniProtKB/TrEMBL
InterPro ASF1-like_sf UniProtKB/TrEMBL
  Histone_chaperone_ASF1-like UniProtKB/TrEMBL
KEGG Report rno:294408 UniProtKB/TrEMBL
NCBI Gene 294408 ENTREZGENE
PANTHER Anti-silence UniProtKB/TrEMBL
Pfam ASF1_hist_chap UniProtKB/TrEMBL
PhenoGen Asf1a PhenoGen
Superfamily-SCOP Anti-silence UniProtKB/TrEMBL
UniProt D3ZFM1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-09-12 Asf1a  anti-silencing function 1A histone chaperone  Asf1a  ASF1 anti-silencing function 1 homolog A (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Asf1a  ASF1 anti-silencing function 1 homolog A (S. cerevisiae)   Asf1a_predicted  ASF1 anti-silencing function 1 homolog A (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Asf1a_predicted  ASF1 anti-silencing function 1 homolog A (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED