Safb2 (scaffold attachment factor B2) - Rat Genome Database

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Gene: Safb2 (scaffold attachment factor B2) Rattus norvegicus
Analyze
Symbol: Safb2
Name: scaffold attachment factor B2
RGD ID: 1588577
Description: Predicted to enable identical protein binding activity. Predicted to act upstream of or within Sertoli cell differentiation and regulation of androgen receptor signaling pathway. Predicted to be located in nuclear body. Orthologous to human SAFB2 (scaffold attachment factor B2); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC301126; similar to scaffold attachment factor B2
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
GRCr891,482,985 - 1,504,142 (-)NCBIGRCr8
mRatBN7.291,395,852 - 1,417,010 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,387,107 - 1,417,038 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,829,300 - 1,850,445 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,179,457 - 7,200,614 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,134,503 - 6,155,649 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,471,618 - 10,492,775 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,471,742 - 10,490,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,468,545 - 9,498,447 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,096,581 - 7,117,736 (+)NCBICelera
Cytogenetic Map9q11NCBI
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

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:18570454   PMID:19674106   PMID:22658674   PMID:22681889   PMID:26092125  


Genomics

Comparative Map Data
Safb2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,482,985 - 1,504,142 (-)NCBIGRCr8
mRatBN7.291,395,852 - 1,417,010 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,387,107 - 1,417,038 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,829,300 - 1,850,445 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,179,457 - 7,200,614 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,134,503 - 6,155,649 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,471,618 - 10,492,775 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,471,742 - 10,490,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,468,545 - 9,498,447 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,096,581 - 7,117,736 (+)NCBICelera
Cytogenetic Map9q11NCBI
SAFB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38195,586,999 - 5,622,776 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl195,586,999 - 5,624,046 (-)EnsemblGRCh38hg38GRCh38
GRCh37195,587,010 - 5,622,787 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36195,538,010 - 5,573,938 (-)NCBINCBI36Build 36hg18NCBI36
Build 34195,538,009 - 5,573,762NCBI
Celera195,524,361 - 5,560,295 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef195,348,131 - 5,384,056 (-)NCBIHuRef
CHM1_1195,586,583 - 5,622,530 (-)NCBICHM1_1
T2T-CHM13v2.0195,573,679 - 5,609,458 (-)NCBIT2T-CHM13v2.0
Safb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,867,971 - 56,891,673 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,867,965 - 56,891,585 (-)EnsemblGRCm39 Ensembl
GRCm381756,560,971 - 56,584,675 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,560,965 - 56,584,585 (-)EnsemblGRCm38mm10GRCm38
MGSCv371756,702,365 - 56,724,006 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361756,247,917 - 56,269,640 (-)NCBIMGSCv36mm8
Celera1760,907,150 - 60,928,791 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.39NCBI
Safb2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554953,775,301 - 3,802,642 (+)NCBIChiLan1.0ChiLan1.0
SAFB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2209,983,504 - 10,019,439 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1199,209,677 - 9,245,591 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0194,604,150 - 4,639,991 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1195,539,679 - 5,575,560 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl195,539,679 - 5,575,560 (-)Ensemblpanpan1.1panPan2
SAFB2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12054,381,323 - 54,414,359 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2054,381,378 - 54,414,122 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2054,107,961 - 54,140,898 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02055,037,198 - 55,070,228 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2055,037,243 - 55,091,447 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12054,099,329 - 54,132,155 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02054,579,859 - 54,612,894 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02054,777,442 - 54,810,377 (+)NCBIUU_Cfam_GSD_1.0
Safb2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,612,317 - 214,644,156 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365883,190,629 - 3,223,124 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAFB2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl273,334,561 - 73,392,846 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1273,334,522 - 73,369,361 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2273,905,211 - 73,939,974 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SAFB2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.165,244,072 - 5,281,053 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl65,244,000 - 5,280,932 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660812,824,643 - 2,862,048 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Safb2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248284,557,775 - 4,586,502 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248284,557,687 - 4,586,297 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Safb2
24 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:363
Count of miRNA genes:213
Interacting mature miRNAs:258
Transcripts:ENSRNOT00000072276, ENSRNOT00000072662
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
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat

Markers in Region
RH132051  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,395,938 - 1,396,143 (-)MAPPERmRatBN7.2
Rnor_6.0910,492,484 - 10,492,688NCBIRnor6.0
Rnor_5.099,489,411 - 9,489,615UniSTSRnor5.0
Celera97,117,445 - 7,117,649UniSTS
Cytogenetic Map9q11UniSTS
MARC_16413-16414:1018631384:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,431,196 - 1,431,698 (-)MAPPERmRatBN7.2
mRatBN7.291,408,692 - 1,409,275 (-)MAPPERmRatBN7.2
Rnor_6.0910,456,926 - 10,457,427NCBIRnor6.0
Rnor_6.0910,479,353 - 10,479,935NCBIRnor6.0
Rnor_5.099,476,280 - 9,476,862UniSTSRnor5.0
Rnor_5.099,453,853 - 9,454,354UniSTSRnor5.0
Celera97,104,315 - 7,104,897UniSTS
Celera97,082,138 - 7,082,639UniSTS
Cytogenetic Map9q11UniSTS
UniSTS:237667  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,397,383 - 1,397,640 (-)MAPPERmRatBN7.2
Rnor_6.0910,490,987 - 10,491,243NCBIRnor6.0
Rnor_5.099,487,914 - 9,488,170UniSTSRnor5.0
Celera97,115,948 - 7,116,204UniSTS
Cytogenetic Map9q11UniSTS


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 3 35 49 33 19 33 3 73 33 41 11
Low 8 8 8 8 8 8 1 2 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000072276   ⟹   ENSRNOP00000064994
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,398,184 - 1,417,010 (-)Ensembl
Rnor_6.0 Ensembl910,471,742 - 10,490,416 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097383   ⟹   ENSRNOP00000078754
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,387,597 - 1,417,010 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100300   ⟹   ENSRNOP00000081439
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,387,107 - 1,417,010 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108191   ⟹   ENSRNOP00000083537
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,387,107 - 1,417,038 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115358   ⟹   ENSRNOP00000093323
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,395,852 - 1,417,010 (-)Ensembl
RefSeq Acc Id: NM_001303144   ⟹   NP_001290073
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,482,985 - 1,504,142 (-)NCBI
mRatBN7.291,395,852 - 1,417,010 (-)NCBI
Rnor_6.0910,471,618 - 10,492,775 (+)NCBI
Celera97,096,581 - 7,117,736 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001290073 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83629 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064994.3
  ENSRNOP00000078754.1
  ENSRNOP00000081439.1
  ENSRNOP00000083537.1
  ENSRNOP00000093323
  ENSRNOP00000093323.1
RefSeq Acc Id: NP_001290073   ⟸   NM_001303144
- UniProtKB: A6KQX1 (UniProtKB/TrEMBL),   A0A8I6AJV7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064994   ⟸   ENSRNOT00000072276
RefSeq Acc Id: ENSRNOP00000078754   ⟸   ENSRNOT00000097383
RefSeq Acc Id: ENSRNOP00000093323   ⟸   ENSRNOT00000115358
RefSeq Acc Id: ENSRNOP00000083537   ⟸   ENSRNOT00000108191
RefSeq Acc Id: ENSRNOP00000081439   ⟸   ENSRNOT00000100300
Protein Domains
RRM   SAP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R6E6-F1-model_v2 AlphaFold M0R6E6 1-790 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588577 AgrOrtholog
BioCyc Gene G2FUF-28525 BioCyc
Ensembl Genes ENSRNOG00000049511 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072276.4 UniProtKB/TrEMBL
  ENSRNOT00000097383.1 UniProtKB/TrEMBL
  ENSRNOT00000100300.1 UniProtKB/TrEMBL
  ENSRNOT00000108191.1 UniProtKB/TrEMBL
  ENSRNOT00000115358 ENTREZGENE
  ENSRNOT00000115358.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.720.30 UniProtKB/TrEMBL
  3.30.70.330 UniProtKB/TrEMBL
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_dom UniProtKB/TrEMBL
  SAFB1_2_RBD UniProtKB/TrEMBL
  SAP_dom UniProtKB/TrEMBL
  SAP_dom_sf UniProtKB/TrEMBL
KEGG Report rno:301126 UniProtKB/TrEMBL
NCBI Gene 301126 ENTREZGENE
PANTHER PTHR15683:SF4 UniProtKB/TrEMBL
  SCAFFOLD ATTACHMENT FACTOR B-RELATED UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
  SAP UniProtKB/TrEMBL
PhenoGen Safb2 PhenoGen
PROSITE RRM UniProtKB/TrEMBL
  SAP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000049511 RatGTEx
SMART RRM UniProtKB/TrEMBL
  SAP UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
  SSF68906 UniProtKB/TrEMBL
UniProt A0A8I5ZLW4_RAT UniProtKB/TrEMBL
  A0A8I5ZSJ1_RAT UniProtKB/TrEMBL
  A0A8I5ZW81_RAT UniProtKB/TrEMBL
  A0A8I6AJV7 ENTREZGENE, UniProtKB/TrEMBL
  A6KQX1 ENTREZGENE, UniProtKB/TrEMBL
  M0R6E6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-17 Safb2  scaffold attachment factor B2  LOC301126  similar to scaffold attachment factor B2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC301126  similar to scaffold attachment factor B2      Symbol and Name status set to provisional 70820 PROVISIONAL