Nfatc4 (nuclear factor of activated T-cells 4) - Rat Genome Database

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Gene: Nfatc4 (nuclear factor of activated T-cells 4) Rattus norvegicus
Analyze
Symbol: Nfatc4
Name: nuclear factor of activated T-cells 4
RGD ID: 1310749
Description: Exhibits DNA-binding transcription factor activity; peroxisome proliferator activated receptor binding activity; and transcription factor binding activity. Involved in cellular response to ionomycin and regulation of synaptic plasticity. Localizes to cytosol and nucleus. Human ortholog(s) of this gene implicated in dilated cardiomyopathy. Orthologous to human NFATC4 (nuclear factor of activated T cells 4); PARTICIPATES IN calcineurin signaling pathway; nuclear factor of activated T-cells signaling pathway; B cell receptor signaling pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 20-HETE.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC102552386; NF-AT3; NF-ATc4; nuclear factor of activated T-cells, cytoplasmic 4; nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4; T-cell transcription factor NFAT3; uncharacterized LOC102552386
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
mRatBN7.21529,286,998 - 29,314,610 (+)NCBI
Rnor_6.0 Ensembl1534,493,138 - 34,504,326 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01534,493,163 - 34,502,238 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01538,381,669 - 38,390,744 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41533,969,774 - 33,978,848 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11533,985,319 - 33,994,626 (+)NCBI
Celera1528,880,299 - 28,889,401 (+)NCBICelera
Cytogenetic Map15p13NCBI
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

Cellular Component
cytoplasm  (IDA,NAS)
cytosol  (IDA,ISO)
nuclear speck  (IEA,ISO)
nucleus  (IDA,ISO)
transcription regulator complex  (IBA,ISO)

References

Additional References at PubMed
PMID:8889548   PMID:11439183   PMID:11827959   PMID:12370307   PMID:12750314   PMID:12796475   PMID:16644691   PMID:16803872   PMID:17044076   PMID:17108007   PMID:17229811   PMID:17242187  
PMID:17430895   PMID:18258855   PMID:18354019   PMID:19179536   PMID:19955386   PMID:20092996   PMID:20173049   PMID:20385772   PMID:20530871   PMID:21880741   PMID:22586092   PMID:22977251  
PMID:23407945   PMID:23543060   PMID:23852416   PMID:24389074   PMID:25450864   PMID:26118953   PMID:26945895   PMID:27155398   PMID:29637744   PMID:31486013   PMID:31789412  


Genomics

Comparative Map Data
Nfatc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21529,286,998 - 29,314,610 (+)NCBI
Rnor_6.0 Ensembl1534,493,138 - 34,504,326 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01534,493,163 - 34,502,238 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01538,381,669 - 38,390,744 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41533,969,774 - 33,978,848 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11533,985,319 - 33,994,626 (+)NCBI
Celera1528,880,299 - 28,889,401 (+)NCBICelera
Cytogenetic Map15p13NCBI
NFATC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1424,365,673 - 24,379,604 (+)EnsemblGRCh38hg38GRCh38
GRCh381424,366,911 - 24,379,604 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371424,836,117 - 24,848,810 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361423,907,094 - 23,918,650 (+)NCBINCBI36hg18NCBI36
Build 341423,907,093 - 23,918,648NCBI
Celera144,700,788 - 4,713,452 (+)NCBI
Cytogenetic Map14q12NCBI
HuRef144,950,950 - 4,963,469 (+)NCBIHuRef
CHM1_11424,834,694 - 24,847,385 (+)NCBICHM1_1
Nfatc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391456,062,252 - 56,071,400 (+)NCBIGRCm39mm39
GRCm39 Ensembl1456,060,601 - 56,071,400 (+)Ensembl
GRCm381455,824,795 - 55,833,943 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1455,823,144 - 55,833,943 (+)EnsemblGRCm38mm10GRCm38
MGSCv371456,443,632 - 56,452,780 (+)NCBIGRCm37mm9NCBIm37
MGSCv361454,779,079 - 54,788,014 (+)NCBImm8
Celera1453,626,552 - 53,635,649 (+)NCBICelera
Cytogenetic Map14C3NCBI
Nfatc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540935,931,173 - 35,940,696 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540935,931,208 - 35,941,555 (-)NCBIChiLan1.0ChiLan1.0
NFATC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11423,267,667 - 23,279,249 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1423,266,702 - 23,279,249 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0145,141,699 - 5,156,021 (+)NCBIMhudiblu_PPA_v0panPan3
NFATC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.184,337,098 - 4,346,409 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl84,336,450 - 4,346,100 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha84,259,072 - 4,268,379 (+)NCBI
ROS_Cfam_1.084,448,860 - 4,458,168 (+)NCBI
UMICH_Zoey_3.184,138,640 - 4,147,945 (+)NCBI
UNSW_CanFamBas_1.084,201,033 - 4,210,339 (+)NCBI
UU_Cfam_GSD_1.084,463,303 - 4,472,610 (+)NCBI
Nfatc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864036,201,144 - 36,210,126 (+)NCBI
SpeTri2.0NW_004936722178,866 - 187,847 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NFATC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl774,918,982 - 74,931,348 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1774,918,982 - 74,929,688 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2780,189,893 - 80,200,589 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NFATC4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,352,173 - 1,362,150 (+)NCBI
ChlSab1.1 Ensembl241,352,291 - 1,362,680 (+)Ensembl
Nfatc4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248208,136,231 - 8,145,395 (-)NCBI

Position Markers
D15Got106  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,313,540 - 29,313,785 (+)MAPPER
Rnor_6.01534,501,169 - 34,501,413NCBIRnor6.0
Rnor_5.01538,389,675 - 38,389,919UniSTSRnor5.0
RGSC_v3.41533,977,778 - 33,978,023RGDRGSC3.4
RGSC_v3.41533,977,779 - 33,978,023UniSTSRGSC3.4
RGSC_v3.11533,993,478 - 33,993,723RGD
Celera1528,888,332 - 28,888,576UniSTS
RH 2.0 Map15178.6RGD
Cytogenetic Map15p13UniSTS
RH137353  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,314,375 - 29,314,595 (+)MAPPER
Rnor_6.01534,502,004 - 34,502,223NCBIRnor6.0
Rnor_5.01538,390,510 - 38,390,729UniSTSRnor5.0
RGSC_v3.41533,978,614 - 33,978,833UniSTSRGSC3.4
Celera1528,889,167 - 28,889,386UniSTS
RH 3.4 Map15260.81UniSTS
Cytogenetic Map15p13UniSTS
PMC135666P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,310,058 - 29,310,582 (+)MAPPER
Rnor_6.01534,497,687 - 34,498,210NCBIRnor6.0
Rnor_5.01538,386,193 - 38,386,716UniSTSRnor5.0
RGSC_v3.41533,974,297 - 33,974,820UniSTSRGSC3.4
Celera1528,884,850 - 28,885,373UniSTS
Cytogenetic Map15p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15137708474Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15137708474Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152102134241082727Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152377896946825072Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:164
Count of miRNA genes:129
Interacting mature miRNAs:143
Transcripts:ENSRNOT00000027789
Prediction methods:Microtar, Miranda, Rnahybrid, 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.


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 4 4 4 12 18 28
Low 3 43 53 37 19 37 8 11 62 17 12 11 8
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027789   ⟹   ENSRNOP00000027789
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1534,493,163 - 34,502,238 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089584   ⟹   ENSRNOP00000071490
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1534,493,138 - 34,504,326 (+)Ensembl
RefSeq Acc Id: NM_001107264   ⟹   NP_001100734
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21529,305,535 - 29,314,610 (+)NCBI
Rnor_6.01534,493,163 - 34,502,238 (+)NCBI
Rnor_5.01538,381,669 - 38,390,744 (+)NCBI
RGSC_v3.41533,969,774 - 33,978,848 (+)RGD
Celera1528,880,299 - 28,889,401 (+)RGD
Sequence:
RefSeq Acc Id: XM_039093302   ⟹   XP_038949230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21529,286,998 - 29,314,600 (+)NCBI
RefSeq Acc Id: XM_039093303   ⟹   XP_038949231
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21529,287,000 - 29,314,600 (+)NCBI
RefSeq Acc Id: XM_039093304   ⟹   XP_038949232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21529,290,346 - 29,314,600 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100734 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949230 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949231 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949232 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3Z9H7 (Get FASTA)   NCBI Sequence Viewer  
  EDM14287 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100734   ⟸   NM_001107264
- UniProtKB: D3Z9H7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071490   ⟸   ENSRNOT00000089584
RefSeq Acc Id: ENSRNOP00000027789   ⟸   ENSRNOT00000027789
RefSeq Acc Id: XP_038949230   ⟸   XM_039093302
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949231   ⟸   XM_039093303
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949232   ⟸   XM_039093304
- Peptide Label: isoform X3
Protein Domains
IPT/TIG   RHD

Transcriptome

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

Promoters
RGD ID:13699696
Promoter ID:EPDNEW_R10215
Type:multiple initiation site
Name:Nfatc4_2
Description:nuclear factor of activated T-cells 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10216  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01534,493,142 - 34,493,202EPDNEW
RGD ID:13699692
Promoter ID:EPDNEW_R10216
Type:initiation region
Name:Nfatc4_1
Description:nuclear factor of activated T-cells 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R10215  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01534,493,250 - 34,493,310EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:1310749 AgrOrtholog
Ensembl Genes ENSRNOG00000020482 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027789 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071490 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027789 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000089584 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
  2.60.40.340 UniProtKB/Swiss-Prot
InterPro Ig-like_fold UniProtKB/Swiss-Prot
  Ig_E-set UniProtKB/Swiss-Prot
  IPT_dom UniProtKB/Swiss-Prot
  NFAT UniProtKB/Swiss-Prot
  p53-like_TF_DNA-bd UniProtKB/Swiss-Prot
  RHD_dimer UniProtKB/Swiss-Prot
  RHD_DNA_bind_dom UniProtKB/Swiss-Prot
  RHD_DNA_bind_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:305897 UniProtKB/Swiss-Prot
NCBI Gene 305897 ENTREZGENE
PANTHER PTHR12533 UniProtKB/Swiss-Prot
Pfam RHD_dimer UniProtKB/Swiss-Prot
  RHD_DNA_bind UniProtKB/Swiss-Prot
PhenoGen Nfatc4 PhenoGen
PRINTS NUCFACTORATC UniProtKB/Swiss-Prot
PROSITE REL_2 UniProtKB/Swiss-Prot
SMART IPT UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49417 UniProtKB/Swiss-Prot
  SSF81296 UniProtKB/Swiss-Prot
UniProt D3Z9H7 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A0A0G2K0L1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Nfatc4  nuclear factor of activated T-cells 4  LOC102552386  uncharacterized LOC102552386  Data Merged 737654 PROVISIONAL
2016-03-29 Nfatc4  nuclear factor of activated T-cells 4  Nfatc4  nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102552386  uncharacterized LOC102552386      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-12-06 Nfatc4  nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4  Nfatc4_predicted  nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Nfatc4_predicted  nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED