Rfx2 (regulatory factor X2) - Rat Genome Database

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Gene: Rfx2 (regulatory factor X2) Rattus norvegicus
Analyze
Symbol: Rfx2
Name: regulatory factor X2
RGD ID: 1588579
Description: Enables DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Orthologous to human RFX2 (regulatory factor X2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DNA-binding protein RFX2; LOC301121; regulatory factor X 2; regulatory factor X, 2 (influences HLA class II expression); similar to DNA-binding protein RFX2
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
GRCr891,691,762 - 1,759,159 (-)NCBIGRCr8
mRatBN7.291,604,636 - 1,671,220 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,604,646 - 1,671,027 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,038,943 - 2,104,978 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,388,045 - 7,454,299 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,344,139 - 6,410,174 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,216,194 - 10,283,467 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,216,205 - 10,283,407 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,214,174 - 9,280,547 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,845,855 - 6,911,961 (+)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
cytoplasm  (IDA,IEA)
nucleus  (IDA,IEA)

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. GOA pipeline RGD automated data pipeline
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
5. Binding of RFX2 and NF-Y to the testis-specific histone H1t promoter may be required for transcriptional activation in primary spermatocytes. VanWert JM, etal., J Cell Biochem. 2008 Jun 1;104(3):1087-101. doi: 10.1002/jcb.21694.
6. Transcription factor RFX2 is abundant in rat testis and enriched in nuclei of primary spermatocytes where it appears to be required for transcription of the testis-specific histone H1t gene. Wolfe SA, etal., J Cell Biochem. 2006 Oct 15;99(3):735-46.
Additional References at PubMed
PMID:8289803   PMID:12477932   PMID:14743396   PMID:20439489   PMID:26162102   PMID:26248850   PMID:26853561  


Genomics

Comparative Map Data
Rfx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,691,762 - 1,759,159 (-)NCBIGRCr8
mRatBN7.291,604,636 - 1,671,220 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,604,646 - 1,671,027 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,038,943 - 2,104,978 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.097,388,045 - 7,454,299 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.096,344,139 - 6,410,174 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,216,194 - 10,283,467 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,216,205 - 10,283,407 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,214,174 - 9,280,547 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,845,855 - 6,911,961 (+)NCBICelera
Cytogenetic Map9q11NCBI
RFX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38195,993,164 - 6,110,500 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl195,993,164 - 6,199,572 (-)EnsemblGRCh38hg38GRCh38
GRCh37195,993,175 - 6,110,511 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36195,944,175 - 6,061,554 (-)NCBINCBI36Build 36hg18NCBI36
Build 34195,944,174 - 6,061,554NCBI
Celera195,932,140 - 6,049,702 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef195,752,732 - 5,870,047 (-)NCBIHuRef
CHM1_1195,993,439 - 6,110,779 (-)NCBICHM1_1
T2T-CHM13v2.0195,980,648 - 6,099,250 (-)NCBIT2T-CHM13v2.0
Rfx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391757,082,897 - 57,138,102 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1757,082,897 - 57,138,013 (-)EnsemblGRCm39 Ensembl
GRCm381756,775,897 - 56,831,008 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,775,897 - 56,831,013 (-)EnsemblGRCm38mm10GRCm38
MGSCv371756,915,320 - 56,970,431 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361756,461,169 - 56,516,087 (-)NCBIMGSCv36mm8
Celera1761,120,038 - 61,175,702 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.5NCBI
Rfx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554953,452,624 - 3,484,446 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554953,414,737 - 3,485,393 (+)NCBIChiLan1.0ChiLan1.0
RFX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22010,393,337 - 10,600,720 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1199,612,761 - 9,738,120 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0195,013,823 - 5,132,451 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1195,942,100 - 6,000,695 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl195,942,100 - 5,996,094 (-)Ensemblpanpan1.1panPan2
RFX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12054,013,556 - 54,111,783 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2054,070,051 - 54,110,220 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2053,758,212 - 53,855,702 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02054,665,752 - 54,763,320 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2054,665,820 - 54,763,308 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12053,732,222 - 53,829,754 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02054,181,159 - 54,278,638 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02054,410,943 - 54,508,743 (+)NCBIUU_Cfam_GSD_1.0
Rfx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,334,927 - 214,371,503 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365883,464,374 - 3,499,841 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365883,463,226 - 3,499,841 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RFX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl272,950,056 - 73,051,180 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1272,949,859 - 73,051,184 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2273,514,680 - 73,581,229 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RFX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.165,637,086 - 5,758,000 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl65,636,735 - 5,738,133 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660812,284,478 - 2,406,938 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rfx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248284,169,198 - 4,249,235 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248284,127,724 - 4,248,925 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rfx2
158 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:379
Count of miRNA genes:187
Interacting mature miRNAs:230
Transcripts:ENSRNOT00000073025
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


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 4 10 2
Low 3 43 26 10 14 10 8 11 70 30 31 9 8
Below cutoff 30 30 5 30 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000073025   ⟹   ENSRNOP00000064610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,604,646 - 1,671,027 (-)Ensembl
Rnor_6.0 Ensembl910,216,293 - 10,283,407 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084312   ⟹   ENSRNOP00000074363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,604,646 - 1,671,027 (-)Ensembl
Rnor_6.0 Ensembl910,216,205 - 10,282,590 (+)Ensembl
RefSeq Acc Id: NM_001106877   ⟹   NP_001100347
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,691,764 - 1,758,146 (-)NCBI
mRatBN7.291,604,638 - 1,671,021 (-)NCBI
Rnor_6.0910,216,210 - 10,283,315 (+)NCBI
Rnor_5.099,214,174 - 9,280,547 (+)NCBI
Celera96,845,855 - 6,911,961 (+)RGD
Sequence:
RefSeq Acc Id: NM_001413766   ⟹   NP_001400695
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,691,764 - 1,758,146 (-)NCBI
mRatBN7.291,604,638 - 1,671,021 (-)NCBI
RefSeq Acc Id: XM_039083138   ⟹   XP_038939066
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,691,762 - 1,759,159 (-)NCBI
mRatBN7.291,604,636 - 1,671,220 (-)NCBI
RefSeq Acc Id: XM_039083139   ⟹   XP_038939067
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,691,762 - 1,759,159 (-)NCBI
mRatBN7.291,604,636 - 1,671,220 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001100347   ⟸   NM_001106877
- Peptide Label: isoform 2
- UniProtKB: B2GV50 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064610   ⟸   ENSRNOT00000073025
RefSeq Acc Id: ENSRNOP00000074363   ⟸   ENSRNOT00000084312
RefSeq Acc Id: XP_038939067   ⟸   XM_039083139
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939066   ⟸   XM_039083138
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001400695   ⟸   NM_001413766
- Peptide Label: isoform 1
- UniProtKB: A0A0G2K7V5 (UniProtKB/TrEMBL)
Protein Domains
RFX-type winged-helix

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2GV50-F1-model_v2 AlphaFold B2GV50 1-692 view protein structure

Transcriptome

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

Promoters
RGD ID:13696456
Promoter ID:EPDNEW_R6974
Type:multiple initiation site
Name:Rfx2_1
Description:regulatory factor X2
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_6.0910,216,167 - 10,216,227EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588579 AgrOrtholog
BioCyc Gene G2FUF-28511 BioCyc
Ensembl Genes ENSRNOG00000045846 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055014148 UniProtKB/Swiss-Prot
  ENSRNOG00060019528 UniProtKB/Swiss-Prot
  ENSRNOG00065014274 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000073025 ENTREZGENE
  ENSRNOT00000073025.3 UniProtKB/Swiss-Prot
  ENSRNOT00000084312 ENTREZGENE
  ENSRNOT00000084312.2 UniProtKB/TrEMBL
  ENSRNOT00055024357 UniProtKB/Swiss-Prot
  ENSRNOT00060033789 UniProtKB/Swiss-Prot
  ENSRNOT00065023553 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7135787 IMAGE-MGC_LOAD
InterPro DNA-bd_RFX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RFX-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RFX1_trans_act UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:301121 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188120 IMAGE-MGC_LOAD
NCBI Gene 301121 ENTREZGENE
PANTHER DNA-BINDING PROTEIN RFX2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12619 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RFX1_trans_act UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RFX_DNA_binding UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rfx2 PhenoGen
PROSITE RFX_DBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000045846 RatGTEx
  ENSRNOG00055014148 RatGTEx
  ENSRNOG00060019528 RatGTEx
  ENSRNOG00065014274 RatGTEx
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K7V5 ENTREZGENE, UniProtKB/TrEMBL
  B2GV50 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Rfx2  regulatory factor X2  Rfx2  regulatory factor X, 2 (influences HLA class II expression)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Rfx2  regulatory factor X, 2 (influences HLA class II expression)  LOC301121  similar to DNA-binding protein RFX2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC301121  similar to DNA-binding protein RFX2      Symbol and Name status set to provisional 70820 PROVISIONAL