Tfap2b (transcription factor AP-2 beta) - Rat Genome Database

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Gene: Tfap2b (transcription factor AP-2 beta) Rattus norvegicus
Analyze
Symbol: Tfap2b
Name: transcription factor AP-2 beta
RGD ID: 1306321
Description: Exhibits chromatin binding activity. Involved in response to drug and response to lithium ion. Localizes to nucleus. Human ortholog(s) of this gene implicated in Char syndrome and patent ductus arteriosus. Orthologous to human TFAP2B (transcription factor AP-2 beta); INTERACTS WITH 1,2-dimethylhydrazine; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC301285; Tcfap2b; transcription factor AP-2-beta
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
mRatBN7.2921,786,250 - 21,815,785 (+)NCBI
Rnor_6.0 Ensembl925,410,669 - 25,440,411 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0925,410,669 - 25,440,568 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0924,271,604 - 24,302,855 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4918,052,402 - 18,082,202 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1918,049,775 - 18,079,184 (+)NCBI
Celera919,374,332 - 19,403,772 (+)NCBICelera
Cytogenetic Map9q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure development  (IBA)
aorta morphogenesis  (ISO,ISS)
calcium ion homeostasis  (ISO,ISS)
cellular ammonium homeostasis  (ISO,ISS)
cellular creatinine homeostasis  (ISO,ISS)
cellular urea homeostasis  (ISO,ISS)
collecting duct development  (ISO,ISS)
distal tubule development  (ISO,ISS)
ductus arteriosus closure  (ISO,ISS)
fat cell differentiation  (ISO)
forelimb morphogenesis  (ISO,ISS)
glucose homeostasis  (ISO,ISS)
glucose metabolic process  (ISO,ISS)
hindlimb morphogenesis  (ISO,ISS)
kidney development  (ISO,ISS)
magnesium ion homeostasis  (ISO,ISS)
metanephric nephron development  (ISO)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of cell population proliferation  (ISO,ISS)
negative regulation of neuron apoptotic process  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO,ISS)
negative regulation of transcription, DNA-templated  (ISO,ISS)
phosphate ion homeostasis  (ISO,ISS)
positive regulation of cell population proliferation  (ISO,ISS)
positive regulation of neuron apoptotic process  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (ISO,ISS)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of urine volume  (ISO,ISS)
potassium ion homeostasis  (ISO,ISS)
regulation of BMP signaling pathway  (ISO,ISS)
regulation of cell differentiation  (ISO,ISS)
regulation of cell population proliferation  (IBA)
regulation of insulin secretion  (ISO,ISS)
regulation of transcription by RNA polymerase II  (IBA,ISO,ISS)
renal water homeostasis  (ISO,ISS)
response to drug  (IEP)
response to lithium ion  (IEP)
retina layer formation  (ISO)
sensory organ development  (ISO)
skin development  (ISO)
sodium ion homeostasis  (ISO,ISS)
sympathetic nervous system development  (ISO,ISS)

Cellular Component
nucleus  (IBA,IDA,ISO,ISS)

References

Additional References at PubMed
PMID:7555706   PMID:7559606   PMID:9271117   PMID:11505339   PMID:11694877   PMID:12072434   PMID:12169688   PMID:12695560   PMID:15940393   PMID:16373396   PMID:17525748   PMID:19325541  
PMID:20448150   PMID:20607706   PMID:21539825   PMID:21829553  


Genomics

Comparative Map Data
Tfap2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2921,786,250 - 21,815,785 (+)NCBI
Rnor_6.0 Ensembl925,410,669 - 25,440,411 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0925,410,669 - 25,440,568 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0924,271,604 - 24,302,855 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4918,052,402 - 18,082,202 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1918,049,775 - 18,079,184 (+)NCBI
Celera919,374,332 - 19,403,772 (+)NCBICelera
Cytogenetic Map9q13NCBI
TFAP2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl650,818,723 - 50,847,619 (+)EnsemblGRCh38hg38GRCh38
GRCh38650,817,692 - 50,847,619 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37650,786,584 - 50,815,332 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36650,894,398 - 50,923,285 (+)NCBINCBI36hg18NCBI36
Build 34650,894,541 - 50,919,634NCBI
Celera652,342,514 - 52,371,233 (+)NCBI
Cytogenetic Map6p12.3NCBI
HuRef650,517,924 - 50,546,498 (+)NCBIHuRef
CHM1_1650,789,288 - 50,818,174 (+)NCBICHM1_1
Tfap2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39119,279,132 - 19,309,069 (+)NCBIGRCm39mm39
GRCm39 Ensembl119,279,138 - 19,308,800 (+)Ensembl
GRCm38119,208,908 - 19,238,845 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl119,208,914 - 19,238,576 (+)EnsemblGRCm38mm10GRCm38
MGSCv37119,198,995 - 19,228,815 (+)NCBIGRCm37mm9NCBIm37
MGSCv36119,194,128 - 19,223,948 (+)NCBImm8
Celera119,103,515 - 19,133,268 (+)NCBICelera
Cytogenetic Map1A3NCBI
Tfap2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554117,142,607 - 7,170,467 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554117,143,095 - 7,171,285 (-)NCBIChiLan1.0ChiLan1.0
TFAP2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1651,635,899 - 51,664,691 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl651,635,899 - 51,664,691 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0650,376,157 - 50,406,740 (+)NCBIMhudiblu_PPA_v0panPan3
TFAP2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11218,544,176 - 18,574,300 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1218,544,446 - 18,572,902 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1218,436,730 - 18,462,495 (+)NCBI
ROS_Cfam_1.01219,041,005 - 19,071,021 (+)NCBI
UMICH_Zoey_3.11218,549,889 - 18,575,642 (+)NCBI
UNSW_CanFamBas_1.01218,654,100 - 18,679,842 (+)NCBI
UU_Cfam_GSD_1.01218,791,560 - 18,817,345 (+)NCBI
Tfap2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494654,075,431 - 54,104,213 (+)NCBI
SpeTri2.0NW_0049364769,855,992 - 9,884,788 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TFAP2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl744,745,422 - 44,770,609 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1744,745,653 - 44,774,563 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2751,206,179 - 51,235,198 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TFAP2B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11721,599,570 - 21,629,757 (-)NCBI
ChlSab1.1 Ensembl1721,604,067 - 21,628,489 (-)Ensembl
Vero_WHO_p1.0NW_02366604450,760,129 - 50,788,887 (+)NCBI
Tfap2b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248555,353,347 - 5,381,454 (-)NCBI

Position Markers
Tcfap2b  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2921,811,442 - 21,811,921 (+)MAPPER
Rnor_6.0925,436,224 - 25,436,702NCBIRnor6.0
Rnor_5.0924,298,653 - 24,299,131UniSTSRnor5.0
RGSC_v3.4918,078,000 - 18,078,478UniSTSRGSC3.4
Celera919,399,570 - 19,400,048UniSTS
Cytogenetic Map9q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91555490147249201Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91952048945029794Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:739
Count of miRNA genes:290
Interacting mature miRNAs:370
Transcripts:ENSRNOT00000030912
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 37 25 4
Low 12 4 37 10 12
Below cutoff 1 19 15 11 13 11 3 3 22 10 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030912   ⟹   ENSRNOP00000030726
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl925,410,669 - 25,440,384 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090920   ⟹   ENSRNOP00000075514
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl925,410,717 - 25,440,411 (+)Ensembl
RefSeq Acc Id: NM_001106896   ⟹   NP_001100366
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2921,786,258 - 21,815,645 (+)NCBI
Rnor_6.0925,410,669 - 25,440,426 (+)NCBI
Rnor_5.0924,271,604 - 24,302,855 (+)NCBI
RGSC_v3.4918,052,402 - 18,082,202 (+)RGD
Celera919,374,332 - 19,403,772 (+)RGD
Sequence:
RefSeq Acc Id: XM_008766927   ⟹   XP_008765149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2921,786,251 - 21,815,785 (+)NCBI
Rnor_6.0925,410,691 - 25,440,568 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596331   ⟹   XP_017451820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0925,410,690 - 25,440,568 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596332   ⟹   XP_017451821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0925,410,690 - 25,440,568 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596333   ⟹   XP_017451822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0925,410,690 - 25,440,568 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083192   ⟹   XP_038939120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2921,786,250 - 21,815,785 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100366 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765149 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939120 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM18662 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100366   ⟸   NM_001106896
- UniProtKB: D4A505 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765149   ⟸   XM_008766927
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451820   ⟸   XM_017596331
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451822   ⟸   XM_017596333
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017451821   ⟸   XM_017596332
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000075514   ⟸   ENSRNOT00000090920
RefSeq Acc Id: ENSRNOP00000030726   ⟸   ENSRNOT00000030912
RefSeq Acc Id: XP_038939120   ⟸   XM_039083192
- Peptide Label: isoform X2
Protein Domains
TF_AP-2

Transcriptome

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

Promoters
RGD ID:13696575
Promoter ID:EPDNEW_R7096
Type:initiation region
Name:Tfap2b_1
Description:transcription factor AP-2 beta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0925,410,755 - 25,410,815EPDNEW

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)
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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
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)
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
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:1306321 AgrOrtholog
Ensembl Genes ENSRNOG00000011823 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000030726 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075514 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030912 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000090920 UniProtKB/TrEMBL
InterPro TF_AP2 UniProtKB/TrEMBL
  TF_AP2_beta UniProtKB/TrEMBL
  TF_AP2_C UniProtKB/TrEMBL
KEGG Report rno:301285 UniProtKB/TrEMBL
NCBI Gene 301285 ENTREZGENE
PANTHER PTHR10812:SF14 UniProtKB/TrEMBL
  TF_AP2 UniProtKB/TrEMBL
Pfam TF_AP-2 UniProtKB/TrEMBL
PhenoGen Tfap2b PhenoGen
PRINTS AP2BTNSCPFCT UniProtKB/TrEMBL
  AP2TNSCPFCT UniProtKB/TrEMBL
UniProt A0A0G2KAT2_RAT UniProtKB/TrEMBL
  D4A505 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-06-09 Tfap2b  transcription factor AP-2 beta  Tcfap2b  transcription factor AP-2 beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tcfap2b  transcription factor AP-2 beta   Tcfap2b_predicted  transcription factor AP-2 beta (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tcfap2b_predicted  transcription factor AP-2 beta (predicted)      Symbol and Name status set to approved 70820 APPROVED