Dppa4 (developmental pluripotency associated 4) - Rat Genome Database

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Gene: Dppa4 (developmental pluripotency associated 4) Rattus norvegicus
Analyze
Symbol: Dppa4
Name: developmental pluripotency associated 4
RGD ID: 1595070
Description: Predicted to enable chromatin binding activity. Predicted to be involved in system development. Predicted to act upstream of or within lung-associated mesenchyme development. Predicted to be active in nucleus. Orthologous to human DPPA4 (developmental pluripotency associated 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: developmental pluripotency-associated protein 4; LOC685378; similar to developmental pluripotency associated 4 isoform 1
RGD Orthologs
Human
Mouse
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
GRCr81166,033,256 - 66,041,754 (-)NCBIGRCr8
mRatBN7.21152,570,279 - 52,578,779 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1152,570,286 - 52,578,797 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1161,333,413 - 61,341,911 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01153,995,211 - 54,003,709 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01153,150,174 - 53,158,672 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01155,233,416 - 55,242,534 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1155,234,545 - 55,240,241 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01158,396,837 - 58,405,926 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41153,842,178 - 53,850,375 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1152,168,464 - 52,177,582 (-)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA,IEA,ISO)

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21896782  


Genomics

Comparative Map Data
Dppa4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81166,033,256 - 66,041,754 (-)NCBIGRCr8
mRatBN7.21152,570,279 - 52,578,779 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1152,570,286 - 52,578,797 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1161,333,413 - 61,341,911 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01153,995,211 - 54,003,709 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01153,150,174 - 53,158,672 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01155,233,416 - 55,242,534 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1155,234,545 - 55,240,241 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01158,396,837 - 58,405,926 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41153,842,178 - 53,850,375 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1152,168,464 - 52,177,582 (-)NCBICelera
Cytogenetic Map11q21NCBI
DPPA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383109,326,144 - 109,339,636 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3109,326,144 - 109,337,546 (-)EnsemblGRCh38hg38GRCh38
GRCh373109,044,991 - 109,056,393 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363110,527,678 - 110,539,109 (-)NCBINCBI36Build 36hg18NCBI36
Build 343110,527,890 - 110,539,083NCBI
Celera3107,443,668 - 107,455,094 (-)NCBICelera
Cytogenetic Map3q13.13NCBI
HuRef3106,419,328 - 106,430,757 (-)NCBIHuRef
CHM1_13109,009,206 - 109,020,613 (-)NCBICHM1_1
T2T-CHM13v2.03112,046,432 - 112,059,906 (-)NCBIT2T-CHM13v2.0
Dppa4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391648,104,098 - 48,114,655 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1648,104,096 - 48,114,600 (+)EnsemblGRCm39 Ensembl
GRCm381648,283,735 - 48,294,292 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1648,283,733 - 48,294,237 (+)EnsemblGRCm38mm10GRCm38
MGSCv371648,283,848 - 48,294,405 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361648,203,357 - 48,213,914 (+)NCBIMGSCv36mm8
Celera1648,645,745 - 48,656,259 (+)NCBICelera
Cytogenetic Map16B5NCBI
cM Map1630.75NCBI
DPPA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22107,303,571 - 107,314,771 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13107,308,350 - 107,319,554 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03106,452,105 - 106,463,295 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13113,379,023 - 113,390,459 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3113,380,836 - 113,390,400 (-)Ensemblpanpan1.1panPan2
DPPA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13314,483,212 - 14,495,319 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3314,588,461 - 14,599,154 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03314,650,926 - 14,662,518 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13314,519,572 - 14,531,159 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03314,587,602 - 14,598,300 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03315,063,573 - 15,075,165 (-)NCBIUU_Cfam_GSD_1.0
Dppa4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602139,950,008 - 139,957,505 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366452,888,259 - 2,895,735 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366452,888,131 - 2,903,396 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DPPA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13150,165,462 - 150,176,761 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113150,165,485 - 150,176,712 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213159,268,490 - 159,279,870 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DPPA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12271,435,945 - 71,446,490 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2271,435,925 - 71,446,110 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604195,040,567 - 95,051,409 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Dppa4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473139,723,840 - 39,736,652 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Dppa4
66 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:77
Count of miRNA genes:66
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000064614
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111945620576331918Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
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
8 6 49 103 78 81 53 20 53 6 193 86 87 41 59 28

Sequence


Ensembl Acc Id: ENSRNOT00000064614   ⟹   ENSRNOP00000062176
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1152,570,296 - 52,578,755 (-)Ensembl
Rnor_6.0 Ensembl1155,234,545 - 55,240,241 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000094801   ⟹   ENSRNOP00000087811
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1152,570,286 - 52,578,797 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000111954   ⟹   ENSRNOP00000087871
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1152,570,431 - 52,578,453 (-)Ensembl
RefSeq Acc Id: NM_001398884   ⟹   NP_001385813
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81166,033,256 - 66,041,754 (-)NCBI
mRatBN7.21152,570,279 - 52,578,779 (-)NCBI
RefSeq Acc Id: NM_001398885   ⟹   NP_001385814
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81166,033,256 - 66,041,754 (-)NCBI
mRatBN7.21152,570,279 - 52,578,779 (-)NCBI
RefSeq Acc Id: NM_001398886   ⟹   NP_001385815
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81166,033,256 - 66,041,754 (-)NCBI
mRatBN7.21152,570,279 - 52,578,779 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001385813 (Get FASTA)   NCBI Sequence Viewer  
  NP_001385814 (Get FASTA)   NCBI Sequence Viewer  
  NP_001385815 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000062176.3
  ENSRNOP00000087811.1
  ENSRNOP00000087871.1
Ensembl Acc Id: ENSRNOP00000062176   ⟸   ENSRNOT00000064614
Ensembl Acc Id: ENSRNOP00000087811   ⟸   ENSRNOT00000094801
Ensembl Acc Id: ENSRNOP00000087871   ⟸   ENSRNOT00000111954
RefSeq Acc Id: NP_001385813   ⟸   NM_001398884
- Peptide Label: isoform 1
- UniProtKB: D3Z8Y2 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: NP_001385815   ⟸   NM_001398886
- Peptide Label: isoform 3
- UniProtKB: D3Z8Y2 (UniProtKB/Swiss-Prot),   A0A8I6A3U7 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001385814   ⟸   NM_001398885
- Peptide Label: isoform 2
- UniProtKB: D3Z8Y2 (UniProtKB/Swiss-Prot)
Protein Domains
Developmental pluripotency-associated protein 2/4   Developmental pluripotency-associated protein 2/4 C-

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z8Y2-F1-model_v2 AlphaFold D3Z8Y2 1-297 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:1595070 AgrOrtholog
BioCyc Gene G2FUF-21414 BioCyc
Ensembl Genes ENSRNOG00000025404 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064614.3 UniProtKB/TrEMBL
  ENSRNOT00000094801.1 UniProtKB/TrEMBL
  ENSRNOT00000111954.1 UniProtKB/TrEMBL
InterPro Dppa2/4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Dppa2/4_C_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Dppa2/4_central_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 685378 ENTREZGENE
PANTHER PTHR16073 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR16073:SF8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DCR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Dppa2_A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dppa4 PhenoGen
RatGTEx ENSRNOG00000025404 RatGTEx
UniProt A0A096MIU9_RAT UniProtKB/TrEMBL
  A0A8I6A3U7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A4Z5_RAT UniProtKB/TrEMBL
  D3Z8Y2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-26 Dppa4  developmental pluripotency associated 4  LOC685378  similar to developmental pluripotency associated 4 isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC685378  similar to developmental pluripotency associated 4 isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL