GDPD5 (glycerophosphodiester phosphodiesterase domain containing 5) - Rat Genome Database

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Gene: GDPD5 (glycerophosphodiester phosphodiesterase domain containing 5) Chlorocebus sabaeus
Analyze
Symbol: GDPD5
Name: glycerophosphodiester phosphodiesterase domain containing 5
RGD ID: 18751825
Description: ENCODES a protein that exhibits glycerophosphocholine phosphodiesterase activity (ortholog); INVOLVED IN cerebral cortex neuron differentiation (ortholog); negative regulation of Notch signaling pathway (ortholog); neuron differentiation (ortholog); ASSOCIATED WITH 3-methylglutaconic aciduria type 7b (ortholog); intellectual disability (ortholog); FOUND IN axon (ortholog); neuronal cell body (ortholog); perinuclear endoplasmic reticulum (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: glycerophosphodiester phosphodiesterase domain-containing protein 5
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1166,665,496 - 66,755,712 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl166,664,914 - 66,755,692 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604359,050,167 - 59,140,696 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
GDPD5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1166,665,496 - 66,755,712 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl166,664,914 - 66,755,692 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604359,050,167 - 59,140,696 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
GDPD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381175,434,640 - 75,525,941 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1175,434,640 - 75,525,941 (-)EnsemblGRCh38hg38GRCh38
GRCh371175,145,685 - 75,236,986 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361174,823,334 - 74,914,515 (-)NCBINCBI36Build 36hg18NCBI36
Celera1172,453,433 - 72,544,371 (-)NCBICelera
Cytogenetic Map11q13.4-q13.5NCBI
HuRef1171,442,901 - 71,533,639 (-)NCBIHuRef
CHM1_11175,029,256 - 75,120,195 (-)NCBICHM1_1
T2T-CHM13v2.01175,364,149 - 75,455,494 (-)NCBIT2T-CHM13v2.0
Gdpd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39799,027,976 - 99,111,082 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl799,030,621 - 99,111,084 (+)EnsemblGRCm39 Ensembl
GRCm38799,381,463 - 99,461,875 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl799,381,414 - 99,461,877 (+)EnsemblGRCm38mm10GRCm38
MGSCv377106,530,059 - 106,609,494 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36799,255,632 - 99,335,067 (+)NCBIMGSCv36mm8
Celera799,706,372 - 99,785,694 (+)NCBICelera
Cytogenetic Map7E1NCBI
cM Map754.07NCBI
Gdpd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81163,091,844 - 163,173,559 (+)NCBIGRCr8
mRatBN7.21153,679,718 - 153,761,452 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1153,679,718 - 153,761,446 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1161,675,570 - 161,757,340 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01168,855,726 - 168,937,492 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01161,729,254 - 161,811,026 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01164,337,176 - 164,418,056 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1164,380,577 - 164,418,593 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01170,539,698 - 170,619,916 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41156,703,241 - 156,794,530 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1151,764,064 - 151,843,287 (+)NCBICelera
Cytogenetic Map1q32NCBI
Gdpd5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541416,323,058 - 16,416,036 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541416,322,705 - 16,416,036 (+)NCBIChiLan1.0ChiLan1.0
GDPD5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2976,364,943 - 76,456,753 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11177,407,564 - 77,499,367 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01170,494,185 - 70,585,921 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11173,796,347 - 73,885,996 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1173,796,347 - 73,885,996 (-)Ensemblpanpan1.1panPan2
GDPD5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12123,070,875 - 23,157,078 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2123,070,964 - 23,156,532 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2122,837,094 - 22,922,751 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02123,274,317 - 23,359,998 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2123,273,752 - 23,359,996 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12123,072,727 - 23,158,360 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02123,269,021 - 23,354,636 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02123,186,853 - 23,272,545 (+)NCBIUU_Cfam_GSD_1.0
Gdpd5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494762,626,252 - 62,688,459 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364984,225,305 - 4,288,059 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364984,225,855 - 4,288,082 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GDPD5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl99,653,596 - 9,740,286 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.199,653,955 - 9,738,186 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2910,842,153 - 10,883,364 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Gdpd5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248171,596,684 - 1,688,566 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248171,596,687 - 1,689,428 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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

endocrine system hemolymphoid system nervous system
High
Medium 4
Low 36 18 56
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000001944   ⟹   ENSCSAP00000000277
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl166,664,914 - 66,755,692 (-)Ensembl
RefSeq Acc Id: XM_008020175   ⟹   XP_008018366
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1166,666,049 - 66,755,710 (-)NCBI
Vero_WHO_p1.0NW_02366604359,050,168 - 59,140,696 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008020178   ⟹   XP_008018369
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1166,665,496 - 66,755,709 (-)NCBI
Vero_WHO_p1.0NW_02366604359,050,168 - 59,140,696 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038005459   ⟹   XP_037861387
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604359,050,168 - 59,140,696 (+)NCBI
RefSeq Acc Id: XM_038005460   ⟹   XP_037861388
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604359,087,634 - 59,140,696 (+)NCBI
RefSeq Acc Id: XM_038005461   ⟹   XP_037861389
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604359,050,167 - 59,140,696 (+)NCBI
Protein Sequences
Protein RefSeqs XP_008018366 (Get FASTA)   NCBI Sequence Viewer  
  XP_008018369 (Get FASTA)   NCBI Sequence Viewer  
  XP_037861387 (Get FASTA)   NCBI Sequence Viewer  
  XP_037861388 (Get FASTA)   NCBI Sequence Viewer  
  XP_037861389 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000000277.1
Reference Protein Sequences
RefSeq Acc Id: XP_008018369   ⟸   XM_008020178
- Peptide Label: isoform X2
- UniProtKB: A0A0D9QV88 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_008018366   ⟸   XM_008020175
- Peptide Label: isoform X1
- UniProtKB: A0A0D9QV88 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000000277   ⟸   ENSCSAT00000001944
RefSeq Acc Id: XP_037861389   ⟸   XM_038005461
- Peptide Label: isoform X1
- UniProtKB: A0A0D9QV88 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037861387   ⟸   XM_038005459
- Peptide Label: isoform X1
- UniProtKB: A0A0D9QV88 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037861388   ⟸   XM_038005460
- Peptide Label: isoform X1
- UniProtKB: A0A0D9QV88 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000003915 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000001944.1 UniProtKB/TrEMBL
Gene3D-CATH 3.20.20.190 UniProtKB/TrEMBL
InterPro GP_PDE_dom UniProtKB/TrEMBL
  PLC-like_Pdiesterase_TIM-brl UniProtKB/TrEMBL
NCBI Gene GDPD5 ENTREZGENE
PANTHER GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE DOMAIN-CONTAINING PROTEIN 5 UniProtKB/TrEMBL
  GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE UniProtKB/TrEMBL
Pfam GDPD UniProtKB/TrEMBL
  GDPD_2 UniProtKB/TrEMBL
PROSITE GP_PDE UniProtKB/TrEMBL
  PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
Superfamily-SCOP SSF51695 UniProtKB/TrEMBL
UniProt A0A0D9QV88 ENTREZGENE, UniProtKB/TrEMBL