Nfia (nuclear factor I/A) - Rat Genome Database

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Gene: Nfia (nuclear factor I/A) Rattus norvegicus
Analyze
Symbol: Nfia
Name: nuclear factor I/A
RGD ID: 3170
Description: Enables DNA binding activity. Involved in positive regulation of DNA-templated transcription and response to organic cyclic compound. Predicted to be located in cell junction and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in NFIA-related disorder. Orthologous to human NFIA (nuclear factor I A); PARTICIPATES IN forkhead class A signaling pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CCAAT-box-binding transcription factor; CTF; NF-I/A; NF1-A; NFI-A; nuclear factor 1 A-type; nuclear factor 1/A; Nuclear Factor IA; TGGCA-binding protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Candidate Gene For: Bp157
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85117,359,006 - 117,897,391 (+)NCBIGRCr8
mRatBN7.25112,436,655 - 112,781,878 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5112,436,644 - 112,775,885 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5115,002,895 - 115,335,577 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05116,728,227 - 117,060,911 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05116,790,806 - 117,123,482 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05116,421,895 - 116,750,381 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5116,420,690 - 116,751,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05120,364,854 - 120,694,011 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45118,152,938 - 118,507,056 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15118,170,466 - 118,513,317 (+)NCBI
Celera5111,023,750 - 111,350,695 (+)NCBICelera
Cytogenetic Map5q33NCBI
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
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,4-dinitrotoluene  (EXP)
2-ethoxyethanol  (EXP)
2-methoxyethanol  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-vinylcyclohexene dioxide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
butanal  (ISO)
caffeine  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloroprene  (EXP)
choline  (ISO)
chromium(6+)  (ISO)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (EXP)
gentamycin  (EXP)
hydrogen cyanide  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
melphalan  (ISO)
mercury dichloride  (EXP)
methapyrilene  (EXP)
methimazole  (EXP)
methoxychlor  (EXP,ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
ochratoxin A  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
pentanal  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP,ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium cyanide  (ISO)
propiconazole  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
senecionine  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulforaphane  (EXP)
sunitinib  (ISO)
tauroursodeoxycholic acid  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
triadimefon  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
triticonazole  (EXP)
troglitazone  (ISO)
trovafloxacin  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cell junction  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Identification of NFI-binding sites and cloning of NFI-cDNAs suggest a regulatory role for NFI transcription factors in olfactory neuron gene expression. Baumeister H, etal., Brain Res Mol Brain Res 1999 Sep 8;72(1):65-79.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. A complex interplay of positive and negative elements is responsible for the different transcriptional activity of liver NF1 variants. Monaci P, etal., Mol Biol Rep 1995;21(3):147-58.
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. Expression, DNA-binding specificity and transcriptional regulation of nuclear factor 1 family proteins from rat. Osada S, etal., Biochem J 1999 Aug 15;342 ( Pt 1)(21):189-98.
8. Nuclear factor 1 family proteins bind to the silencer element in the rat glutathione transferase P gene. Osada S, etal., J Biochem (Tokyo) 1997 Feb;121(2):355-63.
9. Purification of a NF1-like DNA-binding protein from rat liver and cloning of the corresponding cDNA. Paonessa G, etal., EMBO J 1988 Oct;7(10):3115-23.
10. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Gene expression profiles following exposure to a developmental neurotoxicant, Aroclor 1254: pathway analysis for possible mode(s) of action. Royland JE and Kodavanti PR, Toxicol Appl Pharmacol. 2008 Sep 1;231(2):179-96. Epub 2008 May 6.
15. Localization of 54 rat genes, and definition of new synteny groups conserved in the human and the rat. Szpirer C, etal., Mamm Genome 2000 Sep;11(9):729-35
16. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:8306889   PMID:9056636   PMID:11835404   PMID:12955085   PMID:15123731   PMID:15684392   PMID:16147868   PMID:16169882   PMID:17010934   PMID:17530927   PMID:19706729   PMID:23407945  


Genomics

Comparative Map Data
Nfia
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85117,359,006 - 117,897,391 (+)NCBIGRCr8
mRatBN7.25112,436,655 - 112,781,878 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5112,436,644 - 112,775,885 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5115,002,895 - 115,335,577 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05116,728,227 - 117,060,911 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05116,790,806 - 117,123,482 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05116,421,895 - 116,750,381 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5116,420,690 - 116,751,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05120,364,854 - 120,694,011 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45118,152,938 - 118,507,056 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15118,170,466 - 118,513,317 (+)NCBI
Celera5111,023,750 - 111,350,695 (+)NCBICelera
Cytogenetic Map5q33NCBI
NFIA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38161,077,227 - 61,462,788 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl160,865,259 - 61,462,788 (+)EnsemblGRCh38hg38GRCh38
GRCh37161,542,899 - 61,928,460 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36161,320,881 - 61,694,624 (+)NCBINCBI36Build 36hg18NCBI36
Build 34161,260,315 - 61,634,057NCBI
Celera159,831,591 - 60,216,841 (+)NCBICelera
Cytogenetic Map1p31.3NCBI
HuRef159,635,821 - 60,040,693 (+)NCBIHuRef
CHM1_1161,658,337 - 62,043,823 (+)NCBICHM1_1
T2T-CHM13v2.0160,956,019 - 61,341,601 (+)NCBIT2T-CHM13v2.0
Nfia
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39497,469,534 - 98,007,113 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl497,660,971 - 98,007,111 (+)EnsemblGRCm39 Ensembl
GRCm38497,578,066 - 98,118,876 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl497,772,734 - 98,118,874 (+)EnsemblGRCm38mm10GRCm38
MGSCv37497,248,634 - 97,785,567 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36497,269,917 - 97,604,410 (+)NCBIMGSCv36mm8
Celera495,943,228 - 96,479,959 (+)NCBICelera
Cytogenetic Map4C5- C6NCBI
cM Map445.52NCBI
Nfia
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542327,806,873 - 28,112,268 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542327,799,976 - 28,108,307 (-)NCBIChiLan1.0ChiLan1.0
NFIA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21165,396,653 - 165,778,359 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11164,550,471 - 164,927,450 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0160,331,945 - 60,713,729 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1162,159,978 - 62,534,170 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl161,938,945 - 62,526,753 (+)Ensemblpanpan1.1panPan2
NFIA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1548,489,521 - 49,064,867 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl548,496,773 - 49,064,848 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha548,556,341 - 48,929,909 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0548,679,005 - 49,048,341 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl548,678,684 - 49,048,459 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1548,627,327 - 48,995,641 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0548,573,147 - 48,946,371 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0548,838,229 - 49,211,486 (-)NCBIUU_Cfam_GSD_1.0
Nfia
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505874,245,514 - 74,803,937 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936522615,012 - 957,282 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936522612,357 - 1,171,079 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NFIA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6150,835,494 - 151,426,749 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16150,834,002 - 151,229,773 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26138,764,564 - 139,158,806 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NFIA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12071,573,729 - 72,171,268 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603345,443,121 - 45,829,474 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nfia
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474231,898,892 - 32,189,295 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474231,895,791 - 32,198,156 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nfia
1831 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:441
Count of miRNA genes:236
Interacting mature miRNAs:311
Transcripts:ENSRNOT00000004017
Prediction methods:Microtar, 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
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1582212Livw2Liver weight QTL 23.50.0004liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)599016066119085810Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
7394708Emca11Estrogen-induced mammary cancer QTL 11mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)599753548113061097Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
7794743Bp373Blood pressure QTL 3730.0058arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5112175546116047089Rat

Markers in Region
D5Wox18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25112,450,727 - 112,450,995 (+)MAPPERmRatBN7.2
Rnor_6.05116,425,636 - 116,425,903NCBIRnor6.0
Rnor_5.05120,368,595 - 120,368,862UniSTSRnor5.0
RGSC_v3.45118,168,978 - 118,169,246RGDRGSC3.4
RGSC_v3.45118,168,979 - 118,169,246UniSTSRGSC3.4
RGSC_v3.15118,174,205 - 118,174,472RGD
Celera5111,027,491 - 111,027,762UniSTS
RH 3.4 Map5788.0UniSTS
RH 3.4 Map5788.0RGD
RH 2.0 Map5719.7RGD
Cytogenetic Map5q33-q34UniSTS
RH80440  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25112,513,923 - 112,514,012 (+)MAPPERmRatBN7.2
Rnor_6.05116,488,657 - 116,488,745NCBIRnor6.0
Rnor_5.05120,432,192 - 120,432,280UniSTSRnor5.0
RGSC_v3.45118,244,253 - 118,244,341UniSTSRGSC3.4
Celera5111,089,762 - 111,089,850UniSTS
Cytogenetic Map5q33-q34UniSTS
RH143730  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25112,570,624 - 112,570,776 (+)MAPPERmRatBN7.2
Rnor_6.05116,545,328 - 116,545,479NCBIRnor6.0
Rnor_5.05120,488,863 - 120,489,014UniSTSRnor5.0
RGSC_v3.45118,301,190 - 118,301,341UniSTSRGSC3.4
Celera5111,146,471 - 111,146,622UniSTS
RH 3.4 Map5789.1UniSTS
Cytogenetic Map5q33-q34UniSTS
BI288968  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25112,466,595 - 112,466,784 (+)MAPPERmRatBN7.2
Rnor_6.05116,441,496 - 116,441,684NCBIRnor6.0
Rnor_5.05120,384,343 - 120,384,531UniSTSRnor5.0
RGSC_v3.45118,184,905 - 118,185,093UniSTSRGSC3.4
Celera5111,043,343 - 111,043,531UniSTS
RH 3.4 Map5789.1UniSTS
Cytogenetic Map5q33-q34UniSTS


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 3 42 37 25 15 25 8 10 68 35 31 11 8
Low 1 20 16 4 16 1 6 10
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109303 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB005129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB060652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF112455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF112456 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY572794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473998 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D78017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D78018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D78019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D78020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X13167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000004017   ⟹   ENSRNOP00000004017
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5112,441,846 - 112,775,885 (+)Ensembl
Rnor_6.0 Ensembl5116,421,900 - 116,751,398 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080577   ⟹   ENSRNOP00000069038
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5112,441,846 - 112,678,845 (+)Ensembl
Rnor_6.0 Ensembl5116,421,894 - 116,653,813 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086628   ⟹   ENSRNOP00000073066
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5112,441,846 - 112,775,885 (+)Ensembl
Rnor_6.0 Ensembl5116,421,894 - 116,751,416 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087089   ⟹   ENSRNOP00000073444
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5112,441,743 - 112,775,745 (+)Ensembl
Rnor_6.0 Ensembl5116,420,690 - 116,721,038 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106921   ⟹   ENSRNOP00000082237
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5112,441,743 - 112,731,526 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108479   ⟹   ENSRNOP00000084507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5112,441,846 - 112,775,885 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117135   ⟹   ENSRNOP00000097022
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5112,436,644 - 112,775,885 (+)Ensembl
RefSeq Acc Id: NM_012988   ⟹   NP_037120
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,557,280 - 117,890,378 (+)NCBI
mRatBN7.25112,441,754 - 112,774,868 (+)NCBI
Rnor_6.05116,421,895 - 116,750,381 (+)NCBI
Rnor_5.05120,364,854 - 120,694,011 (+)NCBI
RGSC_v3.45118,152,938 - 118,507,056 (+)RGD
Celera5111,023,750 - 111,350,695 (+)RGD
Sequence:
RefSeq Acc Id: XM_039109300   ⟹   XP_038965228
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,551,857 - 117,897,391 (+)NCBI
mRatBN7.25112,436,655 - 112,781,878 (+)NCBI
RefSeq Acc Id: XM_039109301   ⟹   XP_038965229
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,552,552 - 117,897,391 (+)NCBI
mRatBN7.25112,440,929 - 112,781,878 (+)NCBI
RefSeq Acc Id: XM_039109302   ⟹   XP_038965230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,686,891 - 117,897,391 (+)NCBI
mRatBN7.25112,571,370 - 112,781,878 (+)NCBI
RefSeq Acc Id: XM_039109303   ⟹   XP_038965231
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,563,306 - 117,897,391 (+)NCBI
mRatBN7.25112,459,854 - 112,781,878 (+)NCBI
RefSeq Acc Id: XM_063287181   ⟹   XP_063143251
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,359,114 - 117,897,391 (+)NCBI
RefSeq Acc Id: XM_063287182   ⟹   XP_063143252
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,359,006 - 117,897,391 (+)NCBI
RefSeq Acc Id: XM_063287183   ⟹   XP_063143253
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,359,114 - 117,897,391 (+)NCBI
RefSeq Acc Id: XM_063287184   ⟹   XP_063143254
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,551,857 - 117,897,391 (+)NCBI
RefSeq Acc Id: XM_063287185   ⟹   XP_063143255
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85117,552,550 - 117,897,391 (+)NCBI
Protein Sequences
Protein RefSeqs NP_037120 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965228 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965229 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965230 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965231 (Get FASTA)   NCBI Sequence Viewer  
  XP_063143251 (Get FASTA)   NCBI Sequence Viewer  
  XP_063143252 (Get FASTA)   NCBI Sequence Viewer  
  XP_063143253 (Get FASTA)   NCBI Sequence Viewer  
  XP_063143254 (Get FASTA)   NCBI Sequence Viewer  
  XP_063143255 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF21949 (Get FASTA)   NCBI Sequence Viewer  
  AAF23585 (Get FASTA)   NCBI Sequence Viewer  
  AAS77864 (Get FASTA)   NCBI Sequence Viewer  
  BAA11203 (Get FASTA)   NCBI Sequence Viewer  
  BAA11204 (Get FASTA)   NCBI Sequence Viewer  
  BAA11205 (Get FASTA)   NCBI Sequence Viewer  
  BAA11206 (Get FASTA)   NCBI Sequence Viewer  
  BAA21102 (Get FASTA)   NCBI Sequence Viewer  
  BAB43904 (Get FASTA)   NCBI Sequence Viewer  
  CAA31565 (Get FASTA)   NCBI Sequence Viewer  
  EDL97790 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000004017
  ENSRNOP00000004017.8
  ENSRNOP00000069038.2
  ENSRNOP00000073066.2
  ENSRNOP00000073444
  ENSRNOP00000073444.2
  ENSRNOP00000082237.1
  ENSRNOP00000084507.1
  ENSRNOP00000097022
  ENSRNOP00000097022.1
  ENSRNOP00055009117
  ENSRNOP00060027933
  ENSRNOP00065022497
GenBank Protein P09414 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_037120   ⟸   NM_012988
- UniProtKB: Q54A99 (UniProtKB/Swiss-Prot),   Q63782 (UniProtKB/Swiss-Prot),   P09414 (UniProtKB/Swiss-Prot),   A0A8I6G968 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004017   ⟸   ENSRNOT00000004017
RefSeq Acc Id: ENSRNOP00000069038   ⟸   ENSRNOT00000080577
RefSeq Acc Id: ENSRNOP00000073444   ⟸   ENSRNOT00000087089
RefSeq Acc Id: ENSRNOP00000073066   ⟸   ENSRNOT00000086628
RefSeq Acc Id: XP_038965228   ⟸   XM_039109300
- Peptide Label: isoform X4
- UniProtKB: A0A8I6AR84 (UniProtKB/TrEMBL),   A0A8I6G968 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965229   ⟸   XM_039109301
- Peptide Label: isoform X5
- UniProtKB: A0A0G2K5I9 (UniProtKB/TrEMBL),   Q63573 (UniProtKB/TrEMBL),   A0A8I6G968 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965231   ⟸   XM_039109303
- Peptide Label: isoform X9
- UniProtKB: Q63785 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965230   ⟸   XM_039109302
- Peptide Label: isoform X8
RefSeq Acc Id: ENSRNOP00000082237   ⟸   ENSRNOT00000106921
RefSeq Acc Id: ENSRNOP00000084507   ⟸   ENSRNOT00000108479
RefSeq Acc Id: ENSRNOP00000097022   ⟸   ENSRNOT00000117135
RefSeq Acc Id: XP_063143252   ⟸   XM_063287182
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063143251   ⟸   XM_063287181
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063143253   ⟸   XM_063287183
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063143254   ⟸   XM_063287184
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063143255   ⟸   XM_063287185
- Peptide Label: isoform X7
Protein Domains
CTF/NF-I

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P09414-F1-model_v2 AlphaFold P09414 1-509 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:3170 AgrOrtholog
BioCyc Gene G2FUF-40597 BioCyc
Ensembl Genes ENSRNOG00000006966 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00055007002 UniProtKB/Swiss-Prot
  ENSRNOG00060019690 UniProtKB/Swiss-Prot
  ENSRNOG00065017008 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004017 ENTREZGENE
  ENSRNOT00000004017.8 UniProtKB/TrEMBL
  ENSRNOT00000080577.2 UniProtKB/TrEMBL
  ENSRNOT00000086628.2 UniProtKB/TrEMBL
  ENSRNOT00000087089.2 UniProtKB/TrEMBL
  ENSRNOT00000106921.1 UniProtKB/TrEMBL
  ENSRNOT00000108479.1 UniProtKB/TrEMBL
  ENSRNOT00000117135.1 UniProtKB/TrEMBL
  ENSRNOT00055011582 UniProtKB/Swiss-Prot
  ENSRNOT00060034092 UniProtKB/Swiss-Prot
  ENSRNOT00065028440 UniProtKB/Swiss-Prot
InterPro CTF/NFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTF/NFI_DNA-bd-dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTF/NFI_DNA-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTF/NFI_DNA-bd_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MAD_homology1_Dwarfin-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25492 UniProtKB/Swiss-Prot
NCBI Gene 25492 ENTREZGENE
PANTHER NUCLEAR FACTOR 1 A-TYPE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11492 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CTF_NFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MH1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NfI_DNAbd_pre-N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nfia PhenoGen
PROSITE CTF_NFI_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTF_NFI_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006966 RatGTEx
  ENSRNOG00055007002 RatGTEx
  ENSRNOG00060019690 RatGTEx
  ENSRNOG00065017008 RatGTEx
SMART DWA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC229055
  TC229056
UniProt A0A0G2K4J4_RAT UniProtKB/TrEMBL
  A0A0G2K5I9 ENTREZGENE
  A0A8I6AR84 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6G968 ENTREZGENE, UniProtKB/TrEMBL
  NFIA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q54A99 ENTREZGENE
  Q63573 ENTREZGENE, UniProtKB/TrEMBL
  Q63782 ENTREZGENE
  Q63783_RAT UniProtKB/TrEMBL
  Q63784_RAT UniProtKB/TrEMBL
  Q63785 ENTREZGENE, UniProtKB/TrEMBL
  Q6PWY0_RAT UniProtKB/TrEMBL
  Q9QY89_RAT UniProtKB/TrEMBL
  Q9QY90_RAT UniProtKB/TrEMBL
UniProt Secondary A0A0G2JUB7 UniProtKB/TrEMBL
  A0A0G2K5I9 UniProtKB/TrEMBL
  F1LRV0 UniProtKB/TrEMBL
  Q54A99 UniProtKB/Swiss-Prot
  Q63782 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-11-06 Nfia  nuclear factor I/A    Nuclear Factor IA  Name updated 625702 APPROVED
2002-06-10 Nfia  Nuclear Factor IA      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process involved in negative regulation of glutathione transferase P (GST-P) gene expression 729073