Gdpd2 (glycerophosphodiester phosphodiesterase domain containing 2) - Rat Genome Database

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Gene: Gdpd2 (glycerophosphodiester phosphodiesterase domain containing 2) Rattus norvegicus
Analyze
Symbol: Gdpd2
Name: glycerophosphodiester phosphodiesterase domain containing 2
RGD ID: 1560780
Description: Predicted to enable glycerophosphodiester phosphodiesterase activity. Predicted to be involved in lipid metabolic process and positive regulation of cell differentiation. Predicted to act upstream of or within actin filament organization and positive regulation of osteoblast differentiation. Predicted to be located in actin filament and lamellipodium. Predicted to be active in plasma membrane. Orthologous to human GDPD2 (glycerophosphodiester phosphodiesterase domain containing 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; diuron.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: glycerophosphoinositol inositolphosphodiesterase GDPD2; LOC302421; RGD1560780; similar to osteoblast differentiation promoting factor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X69,866,395 - 69,875,419 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX69,866,799 - 69,875,414 (+)EnsemblGRCr8
mRatBN7.2X65,826,273 - 65,835,361 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX65,826,574 - 65,835,361 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX67,309,957 - 67,318,744 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X70,810,351 - 70,819,138 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X68,371,257 - 68,380,044 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X70,563,381 - 70,572,295 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX70,563,570 - 70,572,295 (+)Ensemblrn6Rnor6.0
Rnor_5.0X71,435,008 - 71,443,913 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X88,744,485 - 88,753,272 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX66,185,410 - 66,194,198 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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:12933806  


Genomics

Comparative Map Data
Gdpd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X69,866,395 - 69,875,419 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX69,866,799 - 69,875,414 (+)EnsemblGRCr8
mRatBN7.2X65,826,273 - 65,835,361 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX65,826,574 - 65,835,361 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX67,309,957 - 67,318,744 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X70,810,351 - 70,819,138 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X68,371,257 - 68,380,044 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X70,563,381 - 70,572,295 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX70,563,570 - 70,572,295 (+)Ensemblrn6Rnor6.0
Rnor_5.0X71,435,008 - 71,443,913 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X88,744,485 - 88,753,272 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX66,185,410 - 66,194,198 (+)NCBICelera
Cytogenetic MapXq22NCBI
GDPD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X70,423,314 - 70,433,381 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX70,423,031 - 70,433,710 (+)Ensemblhg38GRCh38
GRCh37X69,643,164 - 69,653,231 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X69,559,716 - 69,569,956 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X69,426,011 - 69,436,251NCBI
CeleraX69,996,203 - 70,006,563 (+)NCBICelera
Cytogenetic MapXq13.1NCBI
HuRefX63,464,255 - 63,474,606 (+)NCBIHuRef
CHM1_1X69,536,774 - 69,547,134 (+)NCBICHM1_1
T2T-CHM13v2.0X68,856,634 - 68,866,693 (+)NCBIT2T-CHM13v2.0
Gdpd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X99,773,442 - 99,782,507 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX99,773,479 - 99,782,501 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X100,729,836 - 100,738,901 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX100,729,873 - 100,738,895 (+)Ensemblmm10GRCm38
MGSCv37X97,925,186 - 97,934,238 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X96,932,659 - 96,941,612 (+)NCBIMGSCv36mm8
CeleraX87,654,592 - 87,663,644 (+)NCBICelera
Cytogenetic MapXC3NCBI
cM MapX43.72NCBI
Gdpd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554759,972,664 - 9,985,939 (+)Ensembl
ChiLan1.0NW_0049554759,972,797 - 9,983,145 (+)NCBIChiLan1.0ChiLan1.0
GDPD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X70,098,795 - 70,110,408 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X70,102,402 - 70,114,010 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X59,689,983 - 59,701,585 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X69,748,999 - 69,759,364 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX69,748,999 - 69,759,364 (+)EnsemblpanPan2panpan1.1
GDPD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X54,865,674 - 54,875,536 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX54,865,818 - 54,875,530 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX45,692,130 - 45,701,974 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X55,832,324 - 55,842,171 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX55,832,309 - 55,905,961 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X53,801,237 - 53,811,081 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X55,132,316 - 55,142,163 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X55,059,253 - 55,069,100 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Gdpd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X47,286,423 - 47,297,886 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367621,048,586 - 1,060,153 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367621,048,597 - 1,060,085 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GDPD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX56,449,425 - 56,460,392 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X56,449,430 - 56,460,399 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X63,644,264 - 63,655,190 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GDPD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X60,268,125 - 60,279,128 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX60,268,485 - 60,279,796 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660652,112,282 - 2,122,672 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gdpd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624903388,866 - 400,607 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624903388,935 - 399,793 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Gdpd2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X58,729,135 - 58,737,772 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Gdpd2
16 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:175
Count of miRNA genes:136
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000003772
Prediction methods:Miranda, Pita, Pita,Targetscan, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat

Markers in Region
MARC_17127-17128:1021042642:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X65,828,617 - 65,829,001 (+)MAPPERmRatBN7.2
Rnor_6.0X70,565,553 - 70,565,936NCBIRnor6.0
Rnor_5.0X71,437,171 - 71,437,554UniSTSRnor5.0
RGSC_v3.4X88,746,529 - 88,746,912UniSTSRGSC3.4
CeleraX66,187,455 - 66,187,838UniSTS
Cytogenetic MapXq31UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 8 56 144 87 90 59 79 59 6 321 161 11 125 79 83 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000003772   ⟹   ENSRNOP00000003772
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX69,866,799 - 69,875,414 (+)Ensembl
mRatBN7.2 EnsemblX65,826,574 - 65,835,361 (+)Ensembl
Rnor_6.0 EnsemblX70,563,570 - 70,572,295 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076018
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX70,563,728 - 70,566,419 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076302
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX70,567,165 - 70,567,955 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076496
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX70,563,788 - 70,566,686 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000130700   ⟹   ENSRNOP00000107774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX69,866,799 - 69,875,414 (+)Ensembl
RefSeq Acc Id: NM_001106944   ⟹   NP_001100414
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X69,866,632 - 69,875,419 (+)NCBI
mRatBN7.2X65,826,574 - 65,835,361 (+)NCBI
Rnor_6.0X70,563,509 - 70,572,295 (+)NCBI
Rnor_5.0X71,435,008 - 71,443,913 (+)NCBI
RGSC_v3.4X88,744,485 - 88,753,272 (+)RGD
CeleraX66,185,410 - 66,194,198 (+)RGD
Sequence:
RefSeq Acc Id: XM_006257064   ⟹   XP_006257126
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X69,866,396 - 69,875,415 (+)NCBI
mRatBN7.2X65,826,273 - 65,835,357 (+)NCBI
Rnor_6.0X70,563,381 - 70,572,291 (+)NCBI
Rnor_5.0X71,435,008 - 71,443,913 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099593   ⟹   XP_038955521
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X69,866,395 - 69,875,415 (+)NCBI
mRatBN7.2X65,826,836 - 65,835,357 (+)NCBI
RefSeq Acc Id: NP_001100414   ⟸   NM_001106944
- UniProtKB: D3Z9K9 (UniProtKB/TrEMBL),   A6IQ87 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257126   ⟸   XM_006257064
- Peptide Label: isoform X1
- UniProtKB: D3Z9K9 (UniProtKB/TrEMBL),   A6IQ87 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003772   ⟸   ENSRNOT00000003772
RefSeq Acc Id: XP_038955521   ⟸   XM_039099593
- Peptide Label: isoform X1
- UniProtKB: D3Z9K9 (UniProtKB/TrEMBL),   A6IQ87 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000107774   ⟸   ENSRNOT00000130700
Protein Domains
GP-PDE

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z9K9-F1-model_v2 AlphaFold D3Z9K9 1-538 view protein structure

Transcriptome

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

Promoters
RGD ID:13701869
Promoter ID:EPDNEW_R12391
Type:single initiation site
Name:Gdpd2_1
Description:glycerophosphodiester phosphodiesterase domain containing 2
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_6.0X70,563,704 - 70,563,764EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560780 AgrOrtholog
BioCyc Gene G2FUF-2123 BioCyc
Ensembl Genes ENSRNOG00000002800 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003772 ENTREZGENE
  ENSRNOT00000003772.7 UniProtKB/TrEMBL
  ENSRNOT00000130700.1 UniProtKB/TrEMBL
Gene3D-CATH 3.20.20.190 UniProtKB/TrEMBL
InterPro GP_PDE_dom UniProtKB/TrEMBL
  PLC-like_Pdiesterase_TIM-brl UniProtKB/TrEMBL
KEGG Report rno:302421 UniProtKB/TrEMBL
NCBI Gene 302421 ENTREZGENE
PANTHER GLYCEROPHOSPHOINOSITOL INOSITOLPHOSPHODIESTERASE GDPD2 UniProtKB/TrEMBL
  GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE UniProtKB/TrEMBL
Pfam GDPD UniProtKB/TrEMBL
  GDPD_2 UniProtKB/TrEMBL
PhenoGen Gdpd2 PhenoGen
PROSITE GP_PDE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002800 RatGTEx
Superfamily-SCOP PLC-like_Pdiesterase_TIM-brl UniProtKB/TrEMBL
UniProt A0ABK0LW95_RAT UniProtKB/TrEMBL
  A6IQ87 ENTREZGENE, UniProtKB/TrEMBL
  D3Z9K9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Gdpd2  glycerophosphodiester phosphodiesterase domain containing 2   Gdpd2_predicted  glycerophosphodiester phosphodiesterase domain containing 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Gdpd2_predicted  glycerophosphodiester phosphodiesterase domain containing 2 (predicted)  RGD1560780_predicted  similar to osteoblast differentiation promoting factor (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1560780_predicted  similar to osteoblast differentiation promoting factor (predicted)  LOC302421  similar to osteoblast differentiation promoting factor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302421  similar to osteoblast differentiation promoting factor      Symbol and Name status set to provisional 70820 PROVISIONAL