Pgbd5 (piggyBac transposable element derived 5) - Rat Genome Database

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Gene: Pgbd5 (piggyBac transposable element derived 5) Rattus norvegicus
Analyze
Symbol: Pgbd5
Name: piggyBac transposable element derived 5
RGD ID: 1310825
Description: Predicted to enable transposase activity. Predicted to be involved in non-replicative DNA transposition. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human PGBD5 (piggyBac transposable element derived 5); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC292098; piggyBac transposable element-derived protein 5
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
GRCr81969,234,171 - 69,299,315 (-)NCBIGRCr8
mRatBN7.21952,336,751 - 52,401,906 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,336,751 - 52,402,397 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1959,122,078 - 59,187,267 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01959,970,315 - 60,036,388 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,048,532 - 62,113,725 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,126,110 - 57,192,182 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,127,054 - 57,192,095 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01967,834,478 - 67,900,336 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,542,070 - 54,608,511 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11954,546,634 - 54,580,371 (-)NCBI
Celera1951,707,799 - 51,772,592 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IBA,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:24180413   PMID:26406119   PMID:27491780  


Genomics

Comparative Map Data
Pgbd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81969,234,171 - 69,299,315 (-)NCBIGRCr8
mRatBN7.21952,336,751 - 52,401,906 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,336,751 - 52,402,397 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1959,122,078 - 59,187,267 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01959,970,315 - 60,036,388 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,048,532 - 62,113,725 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,126,110 - 57,192,182 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,127,054 - 57,192,095 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01967,834,478 - 67,900,336 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,542,070 - 54,608,511 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11954,546,634 - 54,580,371 (-)NCBI
Celera1951,707,799 - 51,772,592 (-)NCBICelera
Cytogenetic Map19q12NCBI
PGBD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381230,314,490 - 230,426,332 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1230,314,490 - 230,426,332 (-)EnsemblGRCh38hg38GRCh38
GRCh371230,450,236 - 230,562,078 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361228,524,015 - 228,579,990 (-)NCBINCBI36Build 36hg18NCBI36
Build 341226,764,127 - 226,820,102NCBI
Celera1203,723,266 - 203,779,187 (-)NCBICelera
Cytogenetic Map1q42.13NCBI
HuRef1200,957,596 - 201,046,325 (-)NCBIHuRef
HuRef1200,945,651 - 200,953,319 (-)NCBIHuRef
CHM1_11231,729,952 - 231,834,738 (-)NCBICHM1_1
T2T-CHM13v2.01229,693,950 - 229,806,671 (-)NCBIT2T-CHM13v2.0
Pgbd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398125,095,788 - 125,161,230 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8125,095,788 - 125,166,397 (-)EnsemblGRCm39 Ensembl
GRCm388124,369,049 - 124,433,936 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8124,369,049 - 124,439,658 (-)EnsemblGRCm38mm10GRCm38
MGSCv378126,892,949 - 126,957,836 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368127,255,139 - 127,320,026 (-)NCBIMGSCv36mm8
Celera8128,654,449 - 128,719,752 (-)NCBICelera
Cytogenetic Map8E2NCBI
cM Map872.65NCBI
Pgbd5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554928,032,220 - 8,090,898 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554928,032,220 - 8,090,898 (+)NCBIChiLan1.0ChiLan1.0
PGBD5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2118,781,686 - 18,887,031 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1118,974,171 - 19,079,180 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01205,869,632 - 205,974,330 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11210,897,173 - 211,000,549 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1210,897,173 - 211,000,555 (-)Ensemblpanpan1.1panPan2
PGBD5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.148,989,542 - 9,025,836 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl48,989,430 - 9,046,954 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha48,910,647 - 9,017,617 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.048,943,416 - 9,049,944 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl48,942,959 - 9,049,242 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.148,953,894 - 9,060,829 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.049,069,047 - 9,175,572 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.049,296,509 - 9,403,256 (+)NCBIUU_Cfam_GSD_1.0
Pgbd5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934443,701,625 - 43,721,108 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648419,866,802 - 19,886,354 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648419,866,855 - 19,886,330 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PGBD5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1459,842,468 - 59,935,021 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11459,842,653 - 59,935,025 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21464,655,307 - 64,747,538 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PGBD5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12567,581,074 - 67,686,624 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2567,581,073 - 67,686,931 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605569,481,786 - 69,588,201 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pgbd5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477519,007,144 - 19,068,690 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477519,007,463 - 19,068,619 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pgbd5
799 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:229
Count of miRNA genes:159
Interacting mature miRNAs:183
Transcripts:ENSRNOT00000058080
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194997648153225766Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat


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
9 7 41 113 73 72 41 21 41 6 178 80 93 41 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000058080   ⟹   ENSRNOP00000054889
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1952,336,751 - 52,402,397 (-)Ensembl
Rnor_6.0 Ensembl1957,127,054 - 57,192,095 (-)Ensembl
RefSeq Acc Id: NM_001106198   ⟹   NP_001099668
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81969,234,171 - 69,299,315 (-)NCBI
mRatBN7.21952,336,751 - 52,401,906 (-)NCBI
Rnor_6.01957,127,054 - 57,192,095 (-)NCBI
Rnor_5.01967,834,478 - 67,900,336 (-)NCBI
RGSC_v3.41954,542,070 - 54,608,511 (-)RGD
Celera1951,707,799 - 51,772,592 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099668 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96728 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000054889.3
RefSeq Acc Id: NP_001099668   ⟸   NM_001106198
- UniProtKB: A6KJ06 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000054889   ⟸   ENSRNOT00000058080
Protein Domains
PiggyBac transposable element-derived protein

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZSZ4-F1-model_v2 AlphaFold D3ZSZ4 1-409 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:1310825 AgrOrtholog
BioCyc Gene G2FUF-5249 BioCyc
Ensembl Genes ENSRNOG00000026791 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000058080.3 UniProtKB/TrEMBL
InterPro PGBD UniProtKB/TrEMBL
  PGBD5 UniProtKB/TrEMBL
KEGG Report rno:292098 UniProtKB/TrEMBL
NCBI Gene 292098 ENTREZGENE
PANTHER PIGGYBAC TRANSPOSABLE ELEMENT-DERIVED PROTEIN 5 UniProtKB/TrEMBL
  PTHR28576 UniProtKB/TrEMBL
Pfam DDE_Tnp_1_7 UniProtKB/TrEMBL
PhenoGen Pgbd5 PhenoGen
RatGTEx ENSRNOG00000026791 RatGTEx
UniProt A6KJ06 ENTREZGENE, UniProtKB/TrEMBL
  D3ZSZ4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pgbd5  piggyBac transposable element derived 5   Pgbd5_predicted  piggyBac transposable element derived 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pgbd5_predicted  piggyBac transposable element derived 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED