Nfix (nuclear factor I X) - Rat Genome Database

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Gene: Nfix (nuclear factor I X) Rattus norvegicus
Analyze
Symbol: Nfix
Name: nuclear factor I X
RGD ID: 69080
Description: Predicted to have 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 central nervous system development and regulation of transcription by RNA polymerase II. Predicted to localize to nucleoplasm. Human ortholog(s) of this gene implicated in Marshall-Smith syndrome and Sotos syndrome 2. Orthologous to human NFIX (nuclear factor I X); INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: NF1-X1 protein; Nf1x; nuclear factor 1 X; nuclear factor 1 X-type; nuclear factor I/X; nuclear factor I/X (CCAAT-binding transcription factor)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21923,355,388 - 23,450,360 (+)NCBI
Rnor_6.0 Ensembl1925,821,780 - 25,914,696 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01925,818,640 - 25,914,777 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01936,794,504 - 36,890,430 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,018,352 - 25,111,367 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,023,177 - 25,097,311 (+)NCBI
Celera1922,941,014 - 23,001,968 (+)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrobenzenesulfonic acid  (ISO)
2,4-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bosentan  (ISO)
buta-1,3-diene  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chloroprene  (EXP)
chlorpyrifos  (EXP)
choline  (ISO)
cisplatin  (ISO)
copper(II) chloride  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (EXP)
dichromium trioxide  (ISO)
dicrotophos  (ISO)
diuron  (EXP)
doxorubicin  (EXP,ISO)
ethanol  (EXP,ISO)
fenvalerate  (EXP)
fipronil  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gamma-hexachlorocyclohexane  (EXP)
glafenine  (EXP)
hydrogen peroxide  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methoxychlor  (ISO)
N-ethyl-N-nitrosourea  (EXP)
nickel atom  (ISO)
p-toluidine  (EXP)
PCB138  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
phosgene  (ISO)
pirinixic acid  (ISO)
poly(vinylpyrrolidone)  (EXP)
procymidone  (EXP)
progesterone  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
silicon dioxide  (ISO)
silver atom  (EXP)
silver(0)  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP,ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)

References

Additional References at PubMed
PMID:9056636   PMID:9660824   PMID:16147868   PMID:16204235   PMID:19706729   PMID:21800304   PMID:24895400  


Genomics

Comparative Map Data
Nfix
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21923,355,388 - 23,450,360 (+)NCBI
Rnor_6.0 Ensembl1925,821,780 - 25,914,696 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01925,818,640 - 25,914,777 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01936,794,504 - 36,890,430 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,018,352 - 25,111,367 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,023,177 - 25,097,311 (+)NCBI
Celera1922,941,014 - 23,001,968 (+)NCBICelera
Cytogenetic Map19q11NCBI
NFIX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1912,995,475 - 13,098,796 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1912,995,608 - 13,098,796 (+)EnsemblGRCh38hg38GRCh38
GRCh381912,995,475 - 13,098,796 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371913,106,289 - 13,209,610 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361912,967,584 - 13,070,610 (+)NCBINCBI36hg18NCBI36
Build 341912,967,583 - 13,070,610NCBI
Celera1912,996,993 - 13,100,014 (+)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,707,303 - 12,782,249 (+)NCBIHuRef
CHM1_11913,107,626 - 13,210,624 (+)NCBICHM1_1
Nfix
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,431,341 - 85,527,086 (-)NCBIGRCm39mm39
GRCm39 Ensembl885,426,505 - 85,526,973 (-)Ensembl
GRCm38884,704,712 - 84,801,238 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,699,876 - 84,800,344 (-)EnsemblGRCm38mm10GRCm38
MGSCv37887,231,498 - 87,324,239 (-)NCBIGRCm37mm9NCBIm37
MGSCv36887,598,719 - 87,690,245 (-)NCBImm8
Celera889,007,669 - 89,082,215 (-)NCBICelera
Cytogenetic Map8C3NCBI
cM Map841.02NCBI
Nfix
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541532,055,375 - 32,117,833 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541532,055,926 - 32,121,611 (+)NCBIChiLan1.0ChiLan1.0
NFIX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11913,315,482 - 13,402,406 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1913,327,690 - 13,402,406 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01912,557,020 - 12,660,316 (+)NCBIMhudiblu_PPA_v0panPan3
NFIX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12049,117,087 - 49,187,023 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2049,117,943 - 49,214,788 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2048,989,635 - 49,094,158 (-)NCBI
ROS_Cfam_1.02049,634,123 - 49,738,501 (-)NCBI
UMICH_Zoey_3.12048,845,676 - 48,949,981 (-)NCBI
UNSW_CanFamBas_1.02049,272,022 - 49,376,246 (-)NCBI
UU_Cfam_GSD_1.02049,514,448 - 49,619,003 (-)NCBI
Nfix
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118208,221,747 - 208,289,349 (-)NCBI
SpeTri2.0NW_0049366592,065,410 - 2,136,898 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NFIX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl265,954,244 - 66,056,567 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1265,954,808 - 66,056,591 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2266,321,736 - 66,402,215 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NFIX
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1611,705,323 - 11,778,943 (+)NCBI
ChlSab1.1 Ensembl611,706,060 - 11,776,083 (+)Ensembl
Vero_WHO_p1.0NW_0236660748,003,657 - 8,106,509 (-)NCBI
Nfix
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624901551,277 - 645,435 (+)NCBI

Position Markers
NFIX  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01936,862,093 - 36,862,339NCBIRnor5.0
RGSC_v3.41925,046,645 - 25,046,890UniSTSRGSC3.4
Celera1922,941,188 - 22,941,433UniSTS
Cytogenetic Map19q11UniSTS
UniSTS:474756  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21923,383,435 - 23,383,753 (-)MAPPER
Rnor_6.01925,886,456 - 25,886,773NCBIRnor6.0
Rnor_5.01936,862,079 - 36,862,396UniSTSRnor5.0
RGSC_v3.41925,046,588 - 25,046,905UniSTSRGSC3.4
Celera1922,941,131 - 22,941,448UniSTS
Cytogenetic Map19q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19129558305Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19129558305Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191073992926201726Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191593952838798459Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192445572643907843Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61328Eae8Experimental allergic encephalomyelitis QTL 84nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)192445762737140233Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191529452433991703Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127635288Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:32
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000039354
Prediction methods:Miranda, Rnahybrid
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.


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 2 33 30 20 12 20 8 11 64 24 32 11 8
Low 1 8 27 21 7 21 8 11 6
Below cutoff 2 2 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_030866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB012234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB012235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC120246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF112459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000039354   ⟹   ENSRNOP00000034591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1925,821,949 - 25,914,696 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091994   ⟹   ENSRNOP00000071775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1925,821,780 - 25,914,689 (-)Ensembl
RefSeq Acc Id: NM_030866   ⟹   NP_110493
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,355,498 - 23,448,273 (+)NCBI
Rnor_6.01925,821,941 - 25,914,696 (-)NCBI
Rnor_5.01936,794,504 - 36,890,430 (-)NCBI
RGSC_v3.41925,018,352 - 25,111,367 (+)RGD
Celera1922,941,014 - 23,001,968 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255307   ⟹   XP_006255369
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01925,818,640 - 25,914,777 (-)NCBI
Rnor_5.01936,794,504 - 36,890,430 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006255308   ⟹   XP_006255370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01925,818,640 - 25,888,351 (-)NCBI
Rnor_5.01936,794,504 - 36,890,430 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006255310   ⟹   XP_006255372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01925,818,640 - 25,891,153 (-)NCBI
Rnor_5.01936,794,504 - 36,890,430 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772418   ⟹   XP_008770640
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01925,818,640 - 25,914,776 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772419   ⟹   XP_008770641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01925,819,393 - 25,914,774 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098010   ⟹   XP_038953938
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,382,405 - 23,444,145 (+)NCBI
RefSeq Acc Id: XM_039098011   ⟹   XP_038953939
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,382,424 - 23,450,360 (+)NCBI
RefSeq Acc Id: XM_039098012   ⟹   XP_038953940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,382,389 - 23,444,145 (+)NCBI
RefSeq Acc Id: XM_039098013   ⟹   XP_038953941
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,382,826 - 23,448,346 (+)NCBI
RefSeq Acc Id: XM_039098014   ⟹   XP_038953942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,382,826 - 23,444,145 (+)NCBI
RefSeq Acc Id: XM_039098015   ⟹   XP_038953943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,355,388 - 23,444,145 (+)NCBI
RefSeq Acc Id: XM_039098016   ⟹   XP_038953944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,381,807 - 23,444,145 (+)NCBI
RefSeq Acc Id: XM_039098017   ⟹   XP_038953945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,382,826 - 23,448,346 (+)NCBI
RefSeq Acc Id: XM_039098018   ⟹   XP_038953946
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,379,782 - 23,444,145 (+)NCBI
RefSeq Acc Id: XM_039098019   ⟹   XP_038953947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,375,303 - 23,444,145 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_110493   ⟸   NM_030866
- UniProtKB: F2Z3R4 (UniProtKB/TrEMBL),   O70189 (UniProtKB/TrEMBL),   O70190 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255369   ⟸   XM_006255307
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006255372   ⟸   XM_006255310
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006255370   ⟸   XM_006255308
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008770640   ⟸   XM_008772418
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008770641   ⟸   XM_008772419
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000071775   ⟸   ENSRNOT00000091994
RefSeq Acc Id: ENSRNOP00000034591   ⟸   ENSRNOT00000039354
RefSeq Acc Id: XP_038953943   ⟸   XM_039098015
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038953947   ⟸   XM_039098019
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038953946   ⟸   XM_039098018
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038953944   ⟸   XM_039098016
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038953940   ⟸   XM_039098012
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038953938   ⟸   XM_039098010
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953939   ⟸   XM_039098011
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038953941   ⟸   XM_039098013
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038953945   ⟸   XM_039098017
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038953942   ⟸   XM_039098014
- Peptide Label: isoform X4
Protein Domains
CTF/NF-I

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69080 AgrOrtholog
Ensembl Genes ENSRNOG00000002983 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034591 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071775 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039354 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000091994 UniProtKB/TrEMBL
InterPro CTF/NFI UniProtKB/TrEMBL
  CTF/NFI_DNA-bd-dom UniProtKB/TrEMBL
  CTF/NFI_DNA-bd_CS UniProtKB/TrEMBL
  CTF/NFI_DNA-bd_N UniProtKB/TrEMBL
  MAD_homology1_Dwarfin-type UniProtKB/TrEMBL
KEGG Report rno:81524 UniProtKB/TrEMBL
NCBI Gene 81524 ENTREZGENE
PANTHER CTF_NFI UniProtKB/TrEMBL
Pfam CTF_NFI UniProtKB/TrEMBL
  MH1 UniProtKB/TrEMBL
  NfI_DNAbd_pre-N UniProtKB/TrEMBL
PhenoGen Nfix PhenoGen
PROSITE CTF_NFI_1 UniProtKB/TrEMBL
  CTF_NFI_2 UniProtKB/TrEMBL
SMART DWA UniProtKB/TrEMBL
UniProt A0A0G2K1B6_RAT UniProtKB/TrEMBL
  F2Z3R4 ENTREZGENE, UniProtKB/TrEMBL
  O70189 ENTREZGENE, UniProtKB/TrEMBL
  O70190 ENTREZGENE, UniProtKB/TrEMBL
  Q9QY86_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-08 Nfix  nuclear factor I X  Nf1x  nuclear factor 1 X  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-14 Nf1x  nuclear factor 1 X  Nfix  nuclear factor I/X (CCAAT-binding transcription factor)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Nfix  nuclear factor I/X (CCAAT-binding transcription factor)  Nfix  nuclear factor I/X  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Nfix  nuclear factor I/X      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the olfactory nasal mucosa 633408