Pld4 (phospholipase D family, member 4) - Rat Genome Database

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Gene: Pld4 (phospholipase D family, member 4) Rattus norvegicus
Analyze
Symbol: Pld4
Name: phospholipase D family, member 4
RGD ID: 1598308
Description: Predicted to enable single-stranded DNA 5'-3' DNA exonuclease activity. Predicted to be involved in hematopoietic progenitor cell differentiation; phagocytosis; and regulation of cytokine production involved in inflammatory response. Predicted to act upstream of or within establishment of localization in cell. Predicted to be located in early endosome and endoplasmic reticulum membrane. Predicted to be active in several cellular components, including endoplasmic reticulum; phagocytic vesicle; and trans-Golgi network membrane. Orthologous to human PLD4 (phospholipase D family member 4); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 5'-3' exonuclease PLD4; LOC362792; phospholipase D4; similar to phospholipase D family, member 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86137,639,948 - 137,647,462 (+)NCBIGRCr8
mRatBN7.26131,818,860 - 131,827,457 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6131,818,860 - 131,826,376 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6131,988,310 - 131,995,820 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06132,284,650 - 132,292,162 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06131,648,754 - 131,656,147 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.06137,323,713 - 137,331,231 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6137,323,713 - 137,331,231 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06146,329,774 - 146,337,292 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46137,744,704 - 137,752,222 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera6129,364,890 - 129,372,215 (+)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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:12477932   PMID:21085684   PMID:22102906   PMID:24029230  


Genomics

Comparative Map Data
Pld4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86137,639,948 - 137,647,462 (+)NCBIGRCr8
mRatBN7.26131,818,860 - 131,827,457 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6131,818,860 - 131,826,376 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6131,988,310 - 131,995,820 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06132,284,650 - 132,292,162 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06131,648,754 - 131,656,147 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.06137,323,713 - 137,331,231 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6137,323,713 - 137,331,231 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06146,329,774 - 146,337,292 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46137,744,704 - 137,752,222 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera6129,364,890 - 129,372,215 (+)NCBICelera
Cytogenetic Map6q32NCBI
PLD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3814104,924,879 - 104,937,785 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl14104,924,713 - 104,937,761 (+)EnsemblGRCh38hg38GRCh38
GRCh3714105,391,216 - 105,404,122 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3614104,462,232 - 104,470,618 (+)NCBINCBI36Build 36hg18NCBI36
Build 3414104,462,268 - 104,470,618NCBI
Celera1485,445,332 - 85,453,718 (+)NCBICelera
Cytogenetic Map14q32.33NCBI
HuRef1485,585,008 - 85,593,394 (+)NCBIHuRef
CHM1_114105,328,651 - 105,337,037 (+)NCBICHM1_1
T2T-CHM13v2.01499,170,773 - 99,184,262 (+)NCBIT2T-CHM13v2.0
Pld4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912112,727,089 - 112,735,420 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12112,727,089 - 112,735,424 (+)EnsemblGRCm39 Ensembl
GRCm3812112,760,446 - 112,768,986 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12112,760,655 - 112,768,990 (+)EnsemblGRCm38mm10GRCm38
MGSCv3712113,998,866 - 114,007,197 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612113,208,463 - 113,216,794 (+)NCBIMGSCv36mm8
Celera12113,976,446 - 113,984,774 (+)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1261.2NCBI
Pld4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555383,295,937 - 3,303,802 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555383,296,581 - 3,303,187 (+)NCBIChiLan1.0ChiLan1.0
PLD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v215106,109,666 - 106,117,996 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan114105,326,170 - 105,334,498 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01485,574,724 - 85,587,176 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.114105,360,584 - 105,368,931 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl14105,360,584 - 105,369,247 (+)Ensemblpanpan1.1panPan2
PLD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1872,410,076 - 72,417,681 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl872,416,637 - 72,417,384 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha871,914,155 - 71,921,625 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0872,684,030 - 72,691,525 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1872,367,136 - 72,374,542 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0872,410,391 - 72,417,878 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0872,809,787 - 72,817,292 (+)NCBIUU_Cfam_GSD_1.0
Pld4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086401,686,753 - 1,694,420 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936621515,636 - 523,359 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936621515,710 - 523,317 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.27131,340,866 - 131,347,958 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PLD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12482,848,775 - 82,857,359 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2482,851,238 - 82,857,579 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605370,274,769 - 70,283,752 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pld4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624734431,956 - 438,170 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624734432,069 - 439,078 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pld4
96 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:36
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000029017
Prediction methods: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
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6106752656132339866Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6122549046137801795Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6122549046140286318Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6122549046140994061Rat
2312560Pur20Proteinuria QTL 202.10.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6125628133137801795Rat

Markers in Region
RH132624  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26131,826,005 - 131,826,199 (+)MAPPERmRatBN7.2
Rnor_6.06137,330,861 - 137,331,054NCBIRnor6.0
Rnor_5.06146,336,922 - 146,337,115UniSTSRnor5.0
RGSC_v3.46137,751,852 - 137,752,045UniSTSRGSC3.4
Celera6129,371,845 - 129,372,038UniSTS
RH 3.4 Map6783.0UniSTS
Cytogenetic Map6q32UniSTS
RH143811  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26131,826,701 - 131,826,996 (+)MAPPERmRatBN7.2
Rnor_6.06137,331,557 - 137,331,850NCBIRnor6.0
Rnor_5.06146,337,618 - 146,337,911UniSTSRnor5.0
RGSC_v3.46137,752,548 - 137,752,841UniSTSRGSC3.4
Celera6129,372,541 - 129,372,835UniSTS
RH 3.4 Map6783.7UniSTS
Cytogenetic Map6q32UniSTS


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 1 28 18 19 18 26 14 16 11
Low 2 36 29 23 23 8 11 48 21 25 8
Below cutoff 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029017   ⟹   ENSRNOP00000032119
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6131,818,860 - 131,826,376 (+)Ensembl
Rnor_6.0 Ensembl6137,323,713 - 137,331,231 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115557   ⟹   ENSRNOP00000088750
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6131,818,860 - 131,826,376 (+)Ensembl
RefSeq Acc Id: NM_001126288   ⟹   NP_001119760
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86137,639,948 - 137,647,462 (+)NCBI
mRatBN7.26131,818,860 - 131,826,376 (+)NCBI
Rnor_6.06137,323,713 - 137,331,231 (+)NCBI
Rnor_5.06146,329,774 - 146,337,292 (+)NCBI
RGSC_v3.46137,744,704 - 137,752,222 (+)RGD
Celera6129,364,890 - 129,372,215 (+)RGD
Sequence:
RefSeq Acc Id: XM_039112594   ⟹   XP_038968522
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86137,639,978 - 137,647,446 (+)NCBI
mRatBN7.26131,818,877 - 131,827,457 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001119760 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968522 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61906 (Get FASTA)   NCBI Sequence Viewer  
  EDL97419 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032119
  ENSRNOP00000032119.3
  ENSRNOP00000088750.1
Reference Protein Sequences
RefSeq Acc Id: NP_001119760   ⟸   NM_001126288
- UniProtKB: G3V904 (UniProtKB/TrEMBL),   A6KBW2 (UniProtKB/TrEMBL),   B1WBV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000032119   ⟸   ENSRNOT00000029017
RefSeq Acc Id: XP_038968522   ⟸   XM_039112594
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000088750   ⟸   ENSRNOT00000115557
Protein Domains
PLD phosphodiesterase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V904-F1-model_v2 AlphaFold G3V904 1-529 view protein structure

Transcriptome

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

Promoters
RGD ID:13694854
Promoter ID:EPDNEW_R5377
Type:initiation region
Name:Pld4_1
Description:phospholipase D family, member 4
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_6.06137,323,755 - 137,323,815EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1598308 AgrOrtholog
BioCyc Gene G2FUF-35776 BioCyc
Ensembl Genes ENSRNOG00000028566 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029017 ENTREZGENE
  ENSRNOT00000029017.4 UniProtKB/TrEMBL
  ENSRNOT00000115557.1 UniProtKB/TrEMBL
Gene3D-CATH Endonuclease Chain A UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8367484 IMAGE-MGC_LOAD
InterPro PLDc_3 UniProtKB/TrEMBL
  PLipase_D/transphosphatidylase UniProtKB/TrEMBL
KEGG Report rno:362792 UniProtKB/TrEMBL
MGC_CLONE MGC:187627 IMAGE-MGC_LOAD
NCBI Gene 362792 ENTREZGENE
PANTHER 5'-3' EXONUCLEASE PLD4 UniProtKB/TrEMBL
  PHOSPHOLIPASE D - RELATED UniProtKB/TrEMBL
Pfam PLDc UniProtKB/TrEMBL
  PLDc_3 UniProtKB/TrEMBL
PhenoGen Pld4 PhenoGen
PROSITE PLD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028566 RatGTEx
SMART PLDc UniProtKB/TrEMBL
Superfamily-SCOP Phospholipase D/nuclease UniProtKB/TrEMBL
UniProt A0A8I6A8P9_RAT UniProtKB/TrEMBL
  A6KBW2 ENTREZGENE, UniProtKB/TrEMBL
  B1WBV8 ENTREZGENE, UniProtKB/TrEMBL
  G3V904 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Pld4  phospholipase D family, member 4  LOC362792  similar to phospholipase D family, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC362792  similar to phospholipase D family, member 4      Symbol and Name status set to provisional 70820 PROVISIONAL