RFX1 (regulatory factor X1) - Rat Genome Database

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Gene: RFX1 (regulatory factor X1) Sus scrofa
Analyze
Symbol: RFX1
Name: regulatory factor X1
RGD ID: 14051870
Description: ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription factor activity (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN regulation of DNA-templated transcription (inferred); regulation of transcription by RNA polymerase II (inferred); ASSOCIATED WITH genetic disease (ortholog); FOUND IN intracellular membrane-bounded organelle (inferred); nucleoplasm (inferred); nucleus (inferred); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: MODEL
Previously known as: MHC class II regulatory factor RFX1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl265,173,574 - 65,205,548 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1265,173,559 - 65,205,551 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2265,447,808 - 65,479,696 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
RFX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl265,173,574 - 65,205,548 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1265,173,559 - 65,205,551 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2265,447,808 - 65,479,696 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RFX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381913,961,530 - 14,006,816 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1913,961,530 - 14,007,039 (-)EnsemblGRCh38hg38GRCh38
GRCh371914,072,342 - 14,117,132 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361913,933,352 - 13,978,097 (-)NCBINCBI36Build 36hg18NCBI36
Build 341913,933,352 - 13,978,097NCBI
Celera1913,965,968 - 14,010,760 (-)NCBICelera
Cytogenetic Map19p13.12NCBI
HuRef1913,643,610 - 13,688,862 (-)NCBIHuRef
CHM1_11914,072,882 - 14,117,703 (-)NCBICHM1_1
T2T-CHM13v2.01914,087,814 - 14,133,810 (-)NCBIT2T-CHM13v2.0
Rfx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39884,789,787 - 84,823,630 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl884,793,463 - 84,823,621 (+)EnsemblGRCm39 Ensembl
GRCm38884,063,564 - 84,097,001 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,066,834 - 84,096,992 (+)EnsemblGRCm38mm10GRCm38
MGSCv37886,590,735 - 86,620,891 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36886,956,971 - 86,987,107 (+)NCBIMGSCv36mm8
Celera888,362,533 - 88,392,882 (+)NCBICelera
Cytogenetic Map8C2NCBI
cM Map840.28NCBI
Rfx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81940,966,102 - 40,996,809 (-)NCBIGRCr8
mRatBN7.21924,061,336 - 24,092,044 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1924,061,336 - 24,092,044 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1930,882,285 - 30,913,168 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01931,536,694 - 31,567,575 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01933,759,478 - 33,790,302 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01925,181,564 - 25,212,410 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,181,564 - 25,212,410 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,157,621 - 36,189,544 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,745,412 - 25,776,702 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11925,750,237 - 25,781,527 (-)NCBI
Celera1923,609,413 - 23,640,097 (-)NCBICelera
Cytogenetic Map19q11NCBI
Rfx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541532,711,008 - 32,731,034 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541532,710,135 - 32,737,918 (-)NCBIChiLan1.0ChiLan1.0
RFX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22018,890,725 - 18,939,328 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11917,891,603 - 17,937,909 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01913,523,778 - 13,568,770 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11914,252,885 - 14,297,474 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1914,252,885 - 14,285,420 (-)Ensemblpanpan1.1panPan2
RFX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12048,488,325 - 48,519,151 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2048,488,661 - 48,519,370 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2048,362,531 - 48,393,495 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02049,006,268 - 49,037,242 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2049,006,850 - 49,037,035 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12048,217,276 - 48,248,265 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02048,643,773 - 48,674,716 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02048,886,839 - 48,917,839 (+)NCBIUU_Cfam_GSD_1.0
Rfx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118207,670,490 - 207,690,672 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366592,664,580 - 2,684,176 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366592,664,004 - 2,691,688 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RFX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1612,617,135 - 12,662,410 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660746,991,874 - 7,038,060 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rfx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249011,231,878 - 1,252,401 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249011,231,196 - 1,260,008 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RFX1
390 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium
Low 9 3 3 5 2 21 2 3 3
Below cutoff 1 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000015038   ⟹   ENSSSCP00000014633
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl265,173,574 - 65,205,548 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000050995   ⟹   ENSSSCP00000053398
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl265,173,574 - 65,205,548 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000055519   ⟹   ENSSSCP00000044574
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl265,173,682 - 65,205,313 (+)Ensembl
RefSeq Acc Id: XM_005661239   ⟹   XP_005661296
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1265,173,580 - 65,205,551 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013994671   ⟹   XP_013850125
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1265,179,365 - 65,205,551 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013994672   ⟹   XP_013850126
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1265,173,568 - 65,205,551 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021083704   ⟹   XP_020939363
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1265,173,580 - 65,205,551 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021083705   ⟹   XP_020939364
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1265,173,559 - 65,205,551 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_020939364   ⟸   XM_021083705
- Peptide Label: isoform X5
- UniProtKB: A0A287AKP3 (UniProtKB/TrEMBL),   A0A8D2BXV7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013850126   ⟸   XM_013994672
- Peptide Label: isoform X4
- UniProtKB: A0A287AKP3 (UniProtKB/TrEMBL),   A0A8D2BXV7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020939363   ⟸   XM_021083704
- Peptide Label: isoform X1
- UniProtKB: F1SD60 (UniProtKB/TrEMBL),   A0A8D1Q776 (UniProtKB/TrEMBL),   A0A4X1SGJ2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005661296   ⟸   XM_005661239
- Peptide Label: isoform X2
- UniProtKB: A0A8D0U967 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013850125   ⟸   XM_013994671
- Peptide Label: isoform X3
- UniProtKB: A0A8D0U967 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000014633   ⟸   ENSSSCT00000015038
RefSeq Acc Id: ENSSSCP00000053398   ⟸   ENSSSCT00000050995
RefSeq Acc Id: ENSSSCP00000044574   ⟸   ENSSSCT00000055519
Protein Domains
RFX-type winged-helix


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000013764 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00015064020 UniProtKB/TrEMBL
  ENSSSCG00025051474 UniProtKB/TrEMBL
  ENSSSCG00030020664 UniProtKB/TrEMBL
  ENSSSCG00035071554 UniProtKB/TrEMBL
  ENSSSCG00040075980 UniProtKB/TrEMBL
  ENSSSCG00055009816 UniProtKB/TrEMBL
  ENSSSCG00060078718 UniProtKB/TrEMBL
  ENSSSCG00065004552 UniProtKB/TrEMBL
  ENSSSCG00070000686 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000015038 ENTREZGENE
  ENSSSCT00000015038.3 UniProtKB/TrEMBL
  ENSSSCT00000055519.2 UniProtKB/TrEMBL
  ENSSSCT00015085653.1 UniProtKB/TrEMBL
  ENSSSCT00015085872.1 UniProtKB/TrEMBL
  ENSSSCT00025070359.1 UniProtKB/TrEMBL
  ENSSSCT00025070606.1 UniProtKB/TrEMBL
  ENSSSCT00030028565.1 UniProtKB/TrEMBL
  ENSSSCT00030028578.1 UniProtKB/TrEMBL
  ENSSSCT00035096756.1 UniProtKB/TrEMBL
  ENSSSCT00035096773.1 UniProtKB/TrEMBL
  ENSSSCT00040105657.1 UniProtKB/TrEMBL
  ENSSSCT00040105660.1 UniProtKB/TrEMBL
  ENSSSCT00055019208.1 UniProtKB/TrEMBL
  ENSSSCT00055019294.1 UniProtKB/TrEMBL
  ENSSSCT00060108860.1 UniProtKB/TrEMBL
  ENSSSCT00060108864.1 UniProtKB/TrEMBL
  ENSSSCT00065006239.1 UniProtKB/TrEMBL
  ENSSSCT00065006244.1 UniProtKB/TrEMBL
  ENSSSCT00070001292.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro DNA-bd_RFX UniProtKB/TrEMBL
  RFX-like UniProtKB/TrEMBL
  RFX1_trans_act UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene RFX1 ENTREZGENE
PANTHER MHC CLASS II REGULATORY FACTOR RFX1 UniProtKB/TrEMBL
  PTHR12619 UniProtKB/TrEMBL
Pfam RFX1_trans_act UniProtKB/TrEMBL
  RFX_DNA_binding UniProtKB/TrEMBL
PROSITE RFX_DBD UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A0A287AKP3 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1SGJ2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0U967 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1Q776 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D2BXV7 ENTREZGENE, UniProtKB/TrEMBL
  F1SD60 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:92243 ENTREZGENE