Sinhcaf (SIN3-HDAC complex associated factor) - Rat Genome Database

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Gene: Sinhcaf (SIN3-HDAC complex associated factor) Rattus norvegicus
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Symbol: Sinhcaf
Name: SIN3-HDAC complex associated factor
RGD ID: 1595037
Description: Predicted to be involved in negative regulation of cell differentiation; negative regulation of cell migration; and positive regulation of cell population proliferation. Predicted to be part of Sin3-type complex. Orthologous to human SINHCAF (SIN3-HDAC complex associated factor); INTERACTS WITH 17beta-estradiol; 2,3,4,7,8-Pentachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Fam60a; family with sequence similarity 60, member A; LOC100909791; LOC686611; MGC187734; protein FAM60A-like; similar to Protein FAM60A (Tera protein); SIN3-HDAC complex-associated factor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84183,619,647 - 183,644,628 (-)NCBIGRCr8
mRatBN7.24181,888,301 - 181,913,294 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4181,888,312 - 181,910,276 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4188,163,184 - 188,188,284 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04183,947,713 - 183,972,815 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04182,568,207 - 182,593,309 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04183,401,314 - 183,426,439 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4183,401,318 - 183,426,439 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04247,532,024 - 247,556,126 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera4170,356,442 - 170,381,382 (-)NCBICelera
Cytogenetic Map4q44NCBI
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
Sin3-type complex  (IBA,ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:22984288   PMID:28554894  


Genomics

Comparative Map Data
Sinhcaf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84183,619,647 - 183,644,628 (-)NCBIGRCr8
mRatBN7.24181,888,301 - 181,913,294 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4181,888,312 - 181,910,276 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4188,163,184 - 188,188,284 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04183,947,713 - 183,972,815 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04182,568,207 - 182,593,309 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04183,401,314 - 183,426,439 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4183,401,318 - 183,426,439 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04247,532,024 - 247,556,126 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera4170,356,442 - 170,381,382 (-)NCBICelera
Cytogenetic Map4q44NCBI
SINHCAF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381231,280,584 - 31,326,150 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1231,280,584 - 31,327,058 (-)EnsemblGRCh38hg38GRCh38
GRCh371231,433,518 - 31,479,084 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361231,324,785 - 31,370,340 (-)NCBINCBI36Build 36hg18NCBI36
Build 341231,324,784 - 31,370,340NCBI
Celera1211,254,383 - 11,300,023 (-)NCBICelera
Cytogenetic Map12p11.21NCBI
HuRef1231,186,852 - 31,232,433 (-)NCBIHuRef
CHM1_11231,398,520 - 31,444,157 (-)NCBICHM1_1
T2T-CHM13v2.01231,157,116 - 31,202,680 (-)NCBIT2T-CHM13v2.0
Sinhcaf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396148,822,538 - 148,847,968 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6148,822,533 - 148,847,965 (-)EnsemblGRCm39 Ensembl
GRCm386148,921,057 - 148,946,470 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6148,921,035 - 148,946,467 (-)EnsemblGRCm38mm10GRCm38
MGSCv376148,869,579 - 148,894,954 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366148,878,227 - 148,903,602 (-)NCBIMGSCv36mm8
Celera6151,959,092 - 151,984,485 (-)NCBICelera
Cytogenetic Map6G3NCBI
cM Map678.67NCBI
Sinhcaf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555054,365,386 - 4,379,232 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555054,344,465 - 4,377,463 (+)NCBIChiLan1.0ChiLan1.0
SINHCAF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21065,447,437 - 65,492,192 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11265,442,956 - 65,487,773 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01254,914,625 - 54,960,258 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11257,498,428 - 57,544,498 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1257,498,428 - 57,544,489 (+)Ensemblpanpan1.1panPan2
SINHCAF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12717,421,065 - 17,456,628 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2717,429,052 - 17,455,144 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2728,961,376 - 28,996,459 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02717,604,428 - 17,639,788 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2717,604,757 - 17,639,726 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12717,413,787 - 17,449,047 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02717,444,696 - 17,480,029 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02729,114,405 - 29,149,788 (-)NCBIUU_Cfam_GSD_1.0
Sinhcaf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494578,020,954 - 78,055,473 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366074,854,332 - 4,889,999 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SINHCAF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl542,930,521 - 42,985,144 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1542,930,445 - 42,963,604 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SINHCAF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11130,755,143 - 30,797,383 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660694,184,169 - 4,230,836 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sinhcaf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247784,917,195 - 4,947,871 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247784,917,169 - 4,947,880 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sinhcaf
90 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:81
Count of miRNA genes:71
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000071930
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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)4144639524182687754Rat
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)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
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)4144639524182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
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)4144639524182687754Rat
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)4144639524182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat

Markers in Region
D4Rat207  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24181,900,635 - 181,900,813 (+)MAPPERmRatBN7.2
mRatBN7.24181,900,635 - 181,900,813 (-)MAPPERmRatBN7.2
Rnor_6.01618,445,430 - 18,445,607NCBIRnor6.0
Rnor_6.04183,414,218 - 183,414,395NCBIRnor6.0
Rnor_5.01618,323,079 - 18,323,256UniSTSRnor5.0
Rnor_5.04247,544,444 - 247,544,621UniSTSRnor5.0
Celera4170,368,814 - 170,368,991UniSTS
RH 3.4 Map41118.2RGD
RH 3.4 Map41118.2UniSTS
RH 2.0 Map41151.5RGD
SHRSP x BN Map498.8499RGD
BI282073  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04183,424,351 - 183,424,561NCBIRnor6.0
Celera4170,381,181 - 170,381,385UniSTS
RH 3.4 Map41130.44UniSTS
Fam60a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24181,888,596 - 181,889,508 (-)MAPPERmRatBN7.2
Rnor_6.04183,401,605 - 183,403,086NCBIRnor6.0
Rnor_6.01618,456,752 - 18,457,659NCBIRnor6.0
Rnor_5.01618,334,401 - 18,335,308UniSTSRnor5.0
Rnor_5.04247,532,315 - 247,533,312UniSTSRnor5.0
Celera4170,356,733 - 170,357,644UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000071930   ⟹   ENSRNOP00000067114
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4181,888,312 - 181,910,276 (-)Ensembl
Rnor_6.0 Ensembl4183,403,000 - 183,424,449 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000083310   ⟹   ENSRNOP00000071885
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4183,401,318 - 183,426,439 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000089160   ⟹   ENSRNOP00000072156
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4183,401,318 - 183,417,667 (-)Ensembl
RefSeq Acc Id: NM_001134711   ⟹   NP_001128183
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84183,619,652 - 183,641,626 (-)NCBI
mRatBN7.24181,888,306 - 181,910,276 (-)NCBI
Rnor_6.04183,401,314 - 183,417,665 (-)NCBI
Rnor_5.04247,532,024 - 247,556,126 (-)NCBI
Celera4170,356,442 - 170,378,392 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001134712   ⟹   NP_001128184
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84183,619,652 - 183,644,628 (-)NCBI
mRatBN7.24181,888,306 - 181,913,278 (-)NCBI
Rnor_6.04183,401,314 - 183,426,439 (-)NCBI
Rnor_5.04247,532,024 - 247,556,126 (-)NCBI
Celera4170,356,442 - 170,381,382 (-)RGD
Sequence:
RefSeq Acc Id: XM_039108360   ⟹   XP_038964288
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84183,619,647 - 183,644,397 (-)NCBI
mRatBN7.24181,888,301 - 181,913,055 (-)NCBI
RefSeq Acc Id: XM_039108361   ⟹   XP_038964289
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84183,619,647 - 183,643,131 (-)NCBI
mRatBN7.24181,888,301 - 181,911,781 (-)NCBI
RefSeq Acc Id: XM_063286697   ⟹   XP_063142767
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84183,619,647 - 183,643,721 (-)NCBI
RefSeq Acc Id: NP_001128184   ⟸   NM_001134712
- UniProtKB: B4F781 (UniProtKB/TrEMBL),   M0RC11 (UniProtKB/TrEMBL),   A0A9K3Y7U5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001128183   ⟸   NM_001134711
- UniProtKB: B4F781 (UniProtKB/TrEMBL),   M0RC11 (UniProtKB/TrEMBL),   A0A9K3Y7U5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000072156   ⟸   ENSRNOT00000089160
Ensembl Acc Id: ENSRNOP00000071885   ⟸   ENSRNOT00000083310
Ensembl Acc Id: ENSRNOP00000067114   ⟸   ENSRNOT00000071930
RefSeq Acc Id: XP_038964288   ⟸   XM_039108360
- Peptide Label: isoform X1
- UniProtKB: M0RC11 (UniProtKB/TrEMBL),   A0A9K3Y7U5 (UniProtKB/TrEMBL),   B4F781 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038964289   ⟸   XM_039108361
- Peptide Label: isoform X1
- UniProtKB: M0RC11 (UniProtKB/TrEMBL),   A0A9K3Y7U5 (UniProtKB/TrEMBL),   B4F781 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063142767   ⟸   XM_063286697
- Peptide Label: isoform X1
- UniProtKB: A0A9K3Y7U5 (UniProtKB/TrEMBL),   B4F781 (UniProtKB/TrEMBL),   M0RC11 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RC11-F1-model_v2 AlphaFold M0RC11 1-261 view protein structure

Transcriptome

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

Promoters
RGD ID:13693514
Promoter ID:EPDNEW_R4039
Type:initiation region
Name:Sinhcaf_1
Description:SIN3-HDAC complex associated factor
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_6.04183,426,455 - 183,426,515EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595037 AgrOrtholog
BioCyc Gene G2FUF-42371 BioCyc
Ensembl Genes ENSRNOG00000049943 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071930.3 UniProtKB/TrEMBL
InterPro FAM60A UniProtKB/TrEMBL
KEGG Report rno:686611 UniProtKB/TrEMBL
NCBI Gene 686611 ENTREZGENE
PANTHER PTHR13422 UniProtKB/TrEMBL
  SIN3-HDAC COMPLEX-ASSOCIATED FACTOR UniProtKB/TrEMBL
Pfam FAM60A UniProtKB/TrEMBL
PhenoGen Sinhcaf PhenoGen
RatGTEx ENSRNOG00000049943 RatGTEx
UniProt A0A9K3Y7U5 ENTREZGENE, UniProtKB/TrEMBL
  B4F781 ENTREZGENE, UniProtKB/TrEMBL
  M0RC11 ENTREZGENE
UniProt Secondary M0RC11 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Sinhcaf  SIN3-HDAC complex associated factor  LOC100909791  protein FAM60A-like  Data merged from RGD:6501581 737654 PROVISIONAL
2017-07-31 Sinhcaf  SIN3-HDAC complex associated factor  Fam60a  family with sequence similarity 60, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100909791  protein FAM60A-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-10-08 Fam60a  family with sequence similarity 60, member A   LOC686611  similar to Protein FAM60A (Tera protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC686611  similar to Protein FAM60A (Tera protein)      Symbol and Name status set to provisional 70820 PROVISIONAL