Tfap2d (transcription factor AP-2 delta) - Rat Genome Database

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Gene: Tfap2d (transcription factor AP-2 delta) Rattus norvegicus
Analyze
Symbol: Tfap2d
Name: transcription factor AP-2 delta
RGD ID: 1304864
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to act upstream of or within inferior colliculus development; negative regulation of neuron apoptotic process; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of transcription regulator complex. Orthologous to human TFAP2D (transcription factor AP-2 delta); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC301284; Tcfap2d; transcription factor AP-2, delta; transcription factor AP-2-delta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8929,177,096 - 29,241,412 (+)NCBIGRCr8
mRatBN7.2921,680,577 - 21,744,840 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl921,680,577 - 21,740,728 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx930,165,099 - 30,223,175 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0935,311,336 - 35,369,776 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0933,607,510 - 33,665,582 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0925,304,876 - 25,365,151 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl925,304,876 - 25,365,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0924,167,386 - 24,227,643 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4917,936,724 - 18,006,941 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1917,933,765 - 18,004,235 (+)NCBI
Celera919,269,921 - 19,328,727 (+)NCBICelera
Cytogenetic Map9q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11522791   PMID:21858141  


Genomics

Comparative Map Data
Tfap2d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8929,177,096 - 29,241,412 (+)NCBIGRCr8
mRatBN7.2921,680,577 - 21,744,840 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl921,680,577 - 21,740,728 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx930,165,099 - 30,223,175 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0935,311,336 - 35,369,776 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0933,607,510 - 33,665,582 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0925,304,876 - 25,365,151 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl925,304,876 - 25,365,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0924,167,386 - 24,227,643 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4917,936,724 - 18,006,941 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1917,933,765 - 18,004,235 (+)NCBI
Celera919,269,921 - 19,328,727 (+)NCBICelera
Cytogenetic Map9q13NCBI
TFAP2D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38650,713,526 - 50,773,033 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl650,713,526 - 50,773,033 (+)EnsemblGRCh38hg38GRCh38
GRCh37650,681,239 - 50,740,746 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36650,789,216 - 50,848,705 (+)NCBINCBI36Build 36hg18NCBI36
Build 34650,789,215 - 50,848,705NCBI
Celera652,237,300 - 52,296,828 (+)NCBICelera
Cytogenetic Map6p12.3NCBI
HuRef650,413,057 - 50,472,532 (+)NCBIHuRef
CHM1_1650,684,197 - 50,743,722 (+)NCBICHM1_1
T2T-CHM13v2.0650,556,563 - 50,616,124 (+)NCBIT2T-CHM13v2.0
Tfap2d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39119,173,246 - 19,244,172 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl119,173,246 - 19,236,570 (+)EnsemblGRCm39 Ensembl
GRCm38119,103,022 - 19,173,948 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl119,103,022 - 19,166,346 (+)EnsemblGRCm38mm10GRCm38
MGSCv37119,093,103 - 19,156,419 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36119,088,238 - 19,151,552 (+)NCBIMGSCv36mm8
Celera118,998,088 - 19,060,944 (+)NCBICelera
Cytogenetic Map1A3NCBI
cM Map16.08NCBI
Tfap2d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554117,216,832 - 7,276,356 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554117,219,474 - 7,276,350 (-)NCBIChiLan1.0ChiLan1.0
TFAP2D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2565,188,390 - 65,248,031 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1661,053,645 - 61,113,268 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0650,274,808 - 50,332,788 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1651,531,757 - 51,590,888 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl651,531,757 - 51,590,888 (+)Ensemblpanpan1.1panPan2
TFAP2D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11218,447,086 - 18,504,137 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1218,447,105 - 18,504,142 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1218,339,916 - 18,396,664 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01218,944,513 - 19,001,109 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1218,944,275 - 19,001,114 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11218,453,196 - 18,509,808 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01218,557,245 - 18,613,864 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01218,694,770 - 18,751,403 (+)NCBIUU_Cfam_GSD_1.0
Tfap2d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494653,970,148 - 54,027,942 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364769,932,156 - 9,990,037 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364769,933,247 - 9,996,375 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TFAP2D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl744,640,281 - 44,703,562 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1744,640,281 - 44,702,561 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2750,994,878 - 51,057,262 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TFAP2D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11721,671,570 - 21,733,003 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1721,671,752 - 21,727,772 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604450,660,481 - 50,717,179 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tfap2d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248555,431,715 - 5,491,952 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248555,430,283 - 5,491,961 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tfap2d
454 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:25
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000065053
Prediction methods: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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92043051965430519Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91696139840594091Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat


Expression

RNA-SEQ Expression

appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
1 1 86 8 8 3 5 3 1 13 6 85 3 16 5

Sequence


Ensembl Acc Id: ENSRNOT00000065053   ⟹   ENSRNOP00000063362
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl921,680,577 - 21,740,728 (+)Ensembl
Rnor_6.0 Ensembl925,304,876 - 25,365,151 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101279   ⟹   ENSRNOP00000078078
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl921,680,809 - 21,740,728 (+)Ensembl
RefSeq Acc Id: NM_001106895   ⟹   NP_001100365
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8929,177,096 - 29,237,247 (+)NCBI
mRatBN7.2921,680,577 - 21,740,728 (+)NCBI
Rnor_6.0925,304,876 - 25,365,151 (+)NCBI
Rnor_5.0924,167,386 - 24,227,643 (+)NCBI
RGSC_v3.4917,936,724 - 18,006,941 (+)RGD
Celera919,269,921 - 19,328,727 (+)RGD
Sequence:
RefSeq Acc Id: NM_001401661   ⟹   NP_001388590
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8929,177,098 - 29,237,247 (+)NCBI
mRatBN7.2921,680,579 - 21,740,728 (+)NCBI
RefSeq Acc Id: XM_039083189   ⟹   XP_038939117
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8929,178,197 - 29,241,412 (+)NCBI
mRatBN7.2921,681,276 - 21,744,840 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100365 (Get FASTA)   NCBI Sequence Viewer  
  NP_001388590 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939117 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM18663 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000063362.1
  ENSRNOP00000078078.1
RefSeq Acc Id: NP_001100365   ⟸   NM_001106895
- Peptide Label: isoform 2
- UniProtKB: D3ZYF2 (UniProtKB/TrEMBL),   A6JJ69 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000063362   ⟸   ENSRNOT00000065053
RefSeq Acc Id: XP_038939117   ⟸   XM_039083189
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000078078   ⟸   ENSRNOT00000101279
RefSeq Acc Id: NP_001388590   ⟸   NM_001401661
- Peptide Label: isoform 1
- UniProtKB: A0A8I5ZJN7 (UniProtKB/TrEMBL)
Protein Domains
Transcription factor AP-2 C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYF2-F1-model_v2 AlphaFold D3ZYF2 1-286 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:1304864 AgrOrtholog
BioCyc Gene G2FUF-28046 BioCyc
Ensembl Genes ENSRNOG00000011642 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065053.2 UniProtKB/TrEMBL
  ENSRNOT00000101279.1 UniProtKB/TrEMBL
InterPro TF_AP2 UniProtKB/TrEMBL
  TF_AP2_C UniProtKB/TrEMBL
NCBI Gene 301284 ENTREZGENE
PANTHER TF_AP2 UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR AP-2-DELTA UniProtKB/TrEMBL
Pfam TF_AP-2 UniProtKB/TrEMBL
PhenoGen Tfap2d PhenoGen
PRINTS AP2TNSCPFCT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011642 RatGTEx
UniProt A0A8I5ZJN7 ENTREZGENE, UniProtKB/TrEMBL
  A6JJ69 ENTREZGENE, UniProtKB/TrEMBL
  D3ZYF2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-06-09 Tfap2d  transcription factor AP-2 delta  Tcfap2d  transcription factor AP-2, delta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tcfap2d  transcription factor AP-2, delta   Tcfap2d_predicted  transcription factor AP-2, delta (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tcfap2d_predicted  transcription factor AP-2, delta (predicted)      Symbol and Name status set to approved 70820 APPROVED