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

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Gene: Rfx6 (regulatory factor X, 6) Rattus norvegicus
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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 enteroendocrine cell differentiation; glucose homeostasis; and positive regulation of insulin secretion involved in cellular response to glucose stimulus. 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22031,020,221 - 31,073,266 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,019,829 - 31,073,147 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2032,039,052 - 32,084,098 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02031,429,965 - 31,475,008 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02032,171,499 - 32,222,899 (+)NCBIRnor_WKY
Rnor_6.02032,709,282 - 32,764,040 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,717,564 - 32,764,035 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02034,493,868 - 34,548,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42030,344,712 - 30,391,212 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12030,348,823 - 30,404,388 (+)NCBI
Celera2032,442,819 - 32,488,055 (+)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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
mRatBN7.22031,020,221 - 31,073,266 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,019,829 - 31,073,147 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2032,039,052 - 32,084,098 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02031,429,965 - 31,475,008 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02032,171,499 - 32,222,899 (+)NCBIRnor_WKY
Rnor_6.02032,709,282 - 32,764,040 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,717,564 - 32,764,035 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02034,493,868 - 34,548,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42030,344,712 - 30,391,212 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12030,348,823 - 30,404,388 (+)NCBI
Celera2032,442,819 - 32,488,055 (+)NCBICelera
Cytogenetic Map20q11NCBI
RFX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386116,877,242 - 116,932,161 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6116,877,212 - 116,932,161 (+)EnsemblGRCh38hg38GRCh38
GRCh376117,198,405 - 117,253,324 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366117,305,069 - 117,360,007 (+)NCBINCBI36Build 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 Ensembl
GRCm381051,677,760 - 51,730,429 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1051,677,756 - 51,730,432 (+)EnsemblGRCm38mm10GRCm38
MGSCv371051,397,566 - 51,450,235 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361051,373,933 - 51,418,844 (+)NCBIMGSCv36mm8
Celera1052,521,182 - 52,574,032 (+)NCBICelera
Cytogenetic Map10B3NCBI
Rfx6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955436213,809 - 280,577 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955436213,810 - 278,699 (+)NCBIChiLan1.0ChiLan1.0
RFX6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan16134,784,692 - 134,839,546 (+)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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha158,037,221 - 58,092,973 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0157,424,008 - 57,479,757 (+)NCBIROS_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_1.0
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
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479812,735,428 - 12,795,502 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rfx6
427 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
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


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 nervous system renal system reproductive system
High
Medium
Low 3 23 15 15 23 10
Below cutoff 6 21 20 4 20 7 12 30

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030642   ⟹   ENSRNOP00000029306
RefSeq Status:
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
RefSeq Acc Id: ENSRNOT00000102360   ⟹   ENSRNOP00000095759
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2031,019,829 - 31,073,147 (+)Ensembl
RefSeq Acc Id: NM_001106388   ⟹   NP_001099858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22031,028,106 - 31,073,147 (+)NCBI
Rnor_6.02032,717,564 - 32,764,035 (+)NCBI
Rnor_5.02034,493,868 - 34,548,443 (+)NCBI
RGSC_v3.42030,344,712 - 30,391,212 (+)RGD
Celera2032,442,819 - 32,488,055 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256444   ⟹   XP_006256506
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22031,020,221 - 31,073,266 (+)NCBI
Rnor_6.02032,709,282 - 32,764,040 (+)NCBI
Rnor_5.02034,493,868 - 34,548,443 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099858 (Get FASTA)   NCBI Sequence Viewer  
  NP_001401847 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256506 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92948 (Get FASTA)   NCBI Sequence Viewer  
  EDL92949 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099858   ⟸   NM_001106388
- Sequence:
RefSeq Acc Id: XP_006256506   ⟸   XM_006256444
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000029306   ⟸   ENSRNOT00000030642
RefSeq Acc Id: ENSRNOP00000095759   ⟸   ENSRNOT00000102360
Protein Domains
RFX-type winged-helix

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 Protein ENSRNOP00000029306.4 UniProtKB/TrEMBL
  ENSRNOP00000095759 ENTREZGENE
  ENSRNOP00000095759.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030642.5 UniProtKB/TrEMBL
  ENSRNOT00000102360 ENTREZGENE
  ENSRNOT00000102360.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro DNA-bd_RFX UniProtKB/TrEMBL
  RFX-like UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:294395 UniProtKB/TrEMBL
NCBI Gene 294395 ENTREZGENE
PANTHER DNA-BINDING PROTEIN RFX6 UniProtKB/TrEMBL
  PTHR12619 UniProtKB/TrEMBL
Pfam RFX_DNA_binding UniProtKB/TrEMBL
PhenoGen Rfx6 PhenoGen
PROSITE RFX_DBD UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A0A8I6AS29 ENTREZGENE, UniProtKB/TrEMBL
  F1LTN7_RAT UniProtKB/TrEMBL


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 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