Rfx6 (regulatory factor X, 6) - Rat Genome Database

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Gene: Rfx6 (regulatory factor X, 6) Rattus norvegicus
Analyze
Symbol: Rfx6
Name: regulatory factor X, 6
RGD ID: 1307491
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including endocrine pancreas development; positive regulation of insulin secretion involved in cellular response to glucose stimulus; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Orthologous to human RFX6 (regulatory factor X6); INTERACTS WITH 17beta-estradiol; bisphenol A; furan.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DNA-binding protein RFX6; DNA-binding protein RFX6-like; LOC100911315; LOC294395; regulatory factor X domain containing 1; Rfxdc1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82031,562,490 - 31,615,967 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2031,562,490 - 31,615,967 (+)EnsemblGRCr8
mRatBN7.22031,019,784 - 31,073,266 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,019,829 - 31,073,147 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2032,039,052 - 32,084,098 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02031,429,965 - 31,475,008 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02032,171,499 - 32,222,899 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02032,709,282 - 32,764,040 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,717,564 - 32,764,035 (+)Ensemblrn6Rnor6.0
Rnor_5.02034,493,868 - 34,548,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42030,344,712 - 30,391,212 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2032,442,819 - 32,488,055 (+)NCBICelera
RGSC_v3.12030,348,823 - 30,404,388 (+)NCBI
Cytogenetic Map20q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,IEA,ISO)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20148032   PMID:25497100  


Genomics

Comparative Map Data
Rfx6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82031,562,490 - 31,615,967 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2031,562,490 - 31,615,967 (+)EnsemblGRCr8
mRatBN7.22031,019,784 - 31,073,266 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,019,829 - 31,073,147 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2032,039,052 - 32,084,098 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02031,429,965 - 31,475,008 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02032,171,499 - 32,222,899 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02032,709,282 - 32,764,040 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,717,564 - 32,764,035 (+)Ensemblrn6Rnor6.0
Rnor_5.02034,493,868 - 34,548,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42030,344,712 - 30,391,212 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2032,442,819 - 32,488,055 (+)NCBICelera
RGSC_v3.12030,348,823 - 30,404,388 (+)NCBI
Cytogenetic Map20q11NCBI
RFX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386116,877,242 - 116,932,161 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6116,877,212 - 116,932,161 (+)Ensemblhg38GRCh38
GRCh376117,198,405 - 117,253,324 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366117,305,069 - 117,360,007 (+)NCBIBuild 36Build 36hg18NCBI36
Build 346117,305,068 - 117,360,006NCBI
Celera6117,941,504 - 117,996,443 (+)NCBICelera
Cytogenetic Map6q22.1NCBI
HuRef6114,778,057 - 114,833,014 (+)NCBIHuRef
CHM1_16117,462,413 - 117,517,362 (+)NCBICHM1_1
T2T-CHM13v2.06118,061,028 - 118,115,944 (+)NCBIT2T-CHM13v2.0
Rfx6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391051,553,856 - 51,606,525 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1051,553,852 - 51,606,528 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381051,677,760 - 51,730,429 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1051,677,756 - 51,730,432 (+)Ensemblmm10GRCm38
MGSCv371051,397,566 - 51,450,235 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361051,373,933 - 51,418,844 (+)NCBIMGSCv36mm8
Celera1052,521,182 - 52,574,032 (+)NCBICelera
Cytogenetic Map10B3NCBI
cM Map1025.74NCBI
Rfx6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955436213,809 - 280,577 (+)Ensembl
ChiLan1.0NW_004955436213,810 - 278,699 (+)NCBIChiLan1.0ChiLan1.0
RFX6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25136,891,710 - 136,946,638 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16134,784,658 - 134,839,586 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06114,686,132 - 114,741,072 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16118,828,974 - 118,883,884 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6118,828,973 - 118,883,884 (+)EnsemblpanPan2panpan1.1
RFX6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1157,242,563 - 57,297,300 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl157,241,927 - 57,296,546 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha158,037,221 - 58,092,973 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0157,424,008 - 57,479,757 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl157,423,953 - 57,479,108 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1157,318,399 - 57,374,090 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0157,166,427 - 57,222,136 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0157,795,388 - 57,851,127 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Rfx6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946107,987,726 - 108,038,262 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493665894,589 - 145,135 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493665894,589 - 145,135 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RFX6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl144,765,451 - 44,823,510 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1144,765,451 - 44,826,884 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2150,063,694 - 50,102,312 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RFX6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11356,889,160 - 56,948,304 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1356,889,780 - 56,946,413 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604029,226,894 - 29,283,607 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rfx6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479812,736,083 - 12,795,502 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462479812,735,428 - 12,795,502 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Rfx6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11829,165,120 - 29,219,208 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rfx6
637 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:131
Count of miRNA genes:80
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000030642
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202668936256021148Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202074558556021148Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202668936256021148Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202679235356021148Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)201224324249189476Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202668936256021148Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202668936256021148Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 1 11 44 71 58 50 12 50 5 195 51 11 16 78 84 8 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000030642   ⟹   ENSRNOP00000029306
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2031,028,106 - 31,073,147 (+)Ensembl
Rnor_6.0 Ensembl2032,717,564 - 32,764,035 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000102360   ⟹   ENSRNOP00000095759
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2031,562,490 - 31,615,967 (+)Ensembl
mRatBN7.2 Ensembl2031,019,829 - 31,073,147 (+)Ensembl
RefSeq Acc Id: NM_001414918   ⟹   NP_001401847
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,562,490 - 31,615,967 (+)NCBI
mRatBN7.22031,019,784 - 31,073,266 (+)NCBI
RefSeq Acc Id: XM_063279068   ⟹   XP_063135138
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,569,099 - 31,615,963 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001401847 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135138 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92948 (Get FASTA)   NCBI Sequence Viewer  
  EDL92949 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000095759
  ENSRNOP00000095759.1
Ensembl Acc Id: ENSRNOP00000029306   ⟸   ENSRNOT00000030642
Ensembl Acc Id: ENSRNOP00000095759   ⟸   ENSRNOT00000102360
RefSeq Acc Id: NP_001401847   ⟸   NM_001414918
- UniProtKB: A0A8I6AS29 (UniProtKB/TrEMBL),   A6K474 (UniProtKB/TrEMBL),   F1LTN7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135138   ⟸   XM_063279068
- Peptide Label: isoform X1
- UniProtKB: A6K474 (UniProtKB/TrEMBL),   F1LTN7 (UniProtKB/TrEMBL)
Protein Domains
RFX-type winged-helix   RFX1-4/6/8-like BCD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LTN7-F1-model_v2 AlphaFold F1LTN7 1-747 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:1307491 AgrOrtholog
BioCyc Gene G2FUF-3659 BioCyc
Ensembl Genes ENSRNOG00000027949 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000102360 ENTREZGENE
  ENSRNOT00000102360.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro DNA-bd_RFX UniProtKB/TrEMBL
  RFX-like UniProtKB/TrEMBL
  RFX1-4/6/8-like_BCD UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene 294395 ENTREZGENE
PANTHER DNA-BINDING PROTEIN RFX6 UniProtKB/TrEMBL
  PTHR12619 UniProtKB/TrEMBL
Pfam BCD_RFX UniProtKB/TrEMBL
  RFX_DNA_binding UniProtKB/TrEMBL
PhenoGen Rfx6 PhenoGen
PROSITE RFX_DBD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027949 RatGTEx
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A0A8I6AS29 ENTREZGENE, UniProtKB/TrEMBL
  A6K474 ENTREZGENE, UniProtKB/TrEMBL
  F1LTN7 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Rfx6  regulatory factor X, 6  LOC100911315  DNA-binding protein RFX6-like  Data merged from RGD:6493387 737654 PROVISIONAL
2012-07-05 LOC100911315  DNA-binding protein RFX6-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-09-09 Rfx6  regulatory factor X, 6  Rfxdc1  regulatory factor X domain containing 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Rfxdc1  regulatory factor X domain containing 1   Rfxdc1_predicted  regulatory factor X domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rfxdc1_predicted  regulatory factor X domain containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED