Psd4 (pleckstrin and Sec7 domain containing 4) - Rat Genome Database

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Gene: Psd4 (pleckstrin and Sec7 domain containing 4) Rattus norvegicus
Analyze
Symbol: Psd4
Name: pleckstrin and Sec7 domain containing 4
RGD ID: 1310289
Description: Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction. Predicted to be active in ruffle membrane. Orthologous to human PSD4 (pleckstrin and Sec7 domain containing 4); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC311785; MGC124698; PH and SEC7 domain-containing protein 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr8327,535,341 - 27,571,850 (+)NCBIGRCr8
mRatBN7.237,137,069 - 7,173,571 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl37,137,155 - 7,173,571 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx310,240,809 - 10,293,052 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0318,827,042 - 18,879,299 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0317,016,851 - 17,069,110 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.031,478,432 - 1,515,094 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl31,478,525 - 1,514,934 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.031,471,271 - 1,507,922 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.432,622,918 - 2,659,328 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.132,622,661 - 2,658,016 (+)NCBI
Celera31,974,423 - 2,010,749 (+)NCBICelera
Cytogenetic Map3p13NCBI
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

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:19946888   PMID:23603394  


Genomics

Comparative Map Data
Psd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8327,535,341 - 27,571,850 (+)NCBIGRCr8
mRatBN7.237,137,069 - 7,173,571 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl37,137,155 - 7,173,571 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx310,240,809 - 10,293,052 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0318,827,042 - 18,879,299 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0317,016,851 - 17,069,110 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.031,478,432 - 1,515,094 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl31,478,525 - 1,514,934 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.031,471,271 - 1,507,922 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.432,622,918 - 2,659,328 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.132,622,661 - 2,658,016 (+)NCBI
Celera31,974,423 - 2,010,749 (+)NCBICelera
Cytogenetic Map3p13NCBI
PSD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382113,173,971 - 113,209,391 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2113,157,325 - 113,209,396 (+)EnsemblGRCh38hg38GRCh38
GRCh372113,931,548 - 113,966,968 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362113,648,031 - 113,677,148 (+)NCBINCBI36Build 36hg18NCBI36
Build 342113,647,790 - 113,676,908NCBI
Celera2107,316,145 - 107,345,262 (+)NCBICelera
Cytogenetic Map2q14.1NCBI
HuRef2106,385,554 - 106,414,668 (+)NCBIHuRef
CHM1_12113,935,985 - 113,965,077 (+)NCBICHM1_1
T2T-CHM13v2.02113,600,541 - 113,635,966 (+)NCBIT2T-CHM13v2.0
Psd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39224,257,571 - 24,299,882 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl224,257,592 - 24,304,966 (+)EnsemblGRCm39 Ensembl
GRCm38224,367,558 - 24,409,870 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl224,367,580 - 24,414,954 (+)EnsemblGRCm38mm10GRCm38
MGSCv37224,240,917 - 24,264,249 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36224,207,406 - 24,230,738 (+)NCBIMGSCv36mm8
Celera224,104,966 - 24,128,260 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map216.38NCBI
Psd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554701,084,318 - 1,125,080 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554701,084,318 - 1,125,244 (-)NCBIChiLan1.0ChiLan1.0
PSD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21214,987,351 - 15,033,456 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A14,990,116 - 15,036,192 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A88,921,973 - 88,968,297 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A114,111,551 - 114,146,914 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A114,125,643 - 114,145,103 (+)Ensemblpanpan1.1panPan2
PSD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11737,260,358 - 37,292,630 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1737,260,290 - 37,295,356 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1737,030,108 - 37,065,265 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01738,037,999 - 38,073,165 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1738,050,087 - 38,073,163 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11737,173,374 - 37,208,479 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01737,229,902 - 37,265,025 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01737,442,341 - 37,477,724 (+)NCBIUU_Cfam_GSD_1.0
Psd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629282,603,481 - 82,617,919 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049367831,497,988 - 1,512,403 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11416,200,957 - 16,221,345 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660803,458,902 - 3,504,981 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Psd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474913,250,095 - 13,310,750 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474913,250,146 - 13,288,672 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Psd4
103 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:189
Count of miRNA genes:129
Interacting mature miRNAs:152
Transcripts:ENSRNOT00000008161
Prediction methods: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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat

Markers in Region
RH130428  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.237,173,220 - 7,173,407 (+)MAPPERmRatBN7.2
Rnor_6.031,514,584 - 1,514,770NCBIRnor6.0
Rnor_5.031,507,412 - 1,507,598UniSTSRnor5.0
RGSC_v3.432,658,978 - 2,659,164UniSTSRGSC3.4
Celera32,010,399 - 2,010,585UniSTS
Cytogenetic Map3p13UniSTS


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 3 8 19 2 11
Low 25 49 41 41 8 9 40 35 34 8
Below cutoff 18 2 34 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008161   ⟹   ENSRNOP00000008161
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl37,137,155 - 7,173,571 (+)Ensembl
Rnor_6.0 Ensembl31,478,525 - 1,514,934 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099515   ⟹   ENSRNOP00000087791
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl37,150,907 - 7,173,571 (+)Ensembl
RefSeq Acc Id: NM_001134881   ⟹   NP_001128353
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,535,440 - 27,571,850 (+)NCBI
mRatBN7.237,137,155 - 7,173,571 (+)NCBI
Rnor_6.031,478,525 - 1,514,934 (+)NCBI
Rnor_5.031,471,271 - 1,507,922 (+)NCBI
RGSC_v3.432,622,918 - 2,659,328 (+)RGD
Celera31,974,423 - 2,010,749 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233591   ⟹   XP_006233653
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,549,360 - 27,571,765 (+)NCBI
mRatBN7.237,151,075 - 7,173,486 (+)NCBI
Rnor_6.031,492,481 - 1,515,094 (+)NCBI
Rnor_5.031,471,271 - 1,507,922 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233592   ⟹   XP_006233654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,535,341 - 27,571,765 (+)NCBI
mRatBN7.237,137,069 - 7,173,486 (+)NCBI
Rnor_6.031,478,432 - 1,515,094 (+)NCBI
Rnor_5.031,471,271 - 1,507,922 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233593   ⟹   XP_006233655
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,549,360 - 27,571,765 (+)NCBI
mRatBN7.237,151,075 - 7,172,259 (+)NCBI
Rnor_6.031,492,481 - 1,515,094 (+)NCBI
Rnor_5.031,471,271 - 1,507,922 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039105177   ⟹   XP_038961105
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,549,174 - 27,571,765 (+)NCBI
mRatBN7.237,150,886 - 7,173,486 (+)NCBI
RefSeq Acc Id: XM_039105178   ⟹   XP_038961106
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,549,174 - 27,571,765 (+)NCBI
mRatBN7.237,150,886 - 7,173,486 (+)NCBI
RefSeq Acc Id: XM_039105179   ⟹   XP_038961107
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,549,358 - 27,571,765 (+)NCBI
mRatBN7.237,151,073 - 7,172,181 (+)NCBI
RefSeq Acc Id: XM_039105180   ⟹   XP_038961108
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,549,358 - 27,565,137 (+)NCBI
mRatBN7.237,151,073 - 7,166,857 (+)NCBI
RefSeq Acc Id: XM_063283915   ⟹   XP_063139985
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,535,359 - 27,571,765 (+)NCBI
RefSeq Acc Id: XM_063283916   ⟹   XP_063139986
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8327,564,567 - 27,571,765 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001128353   ⟸   NM_001134881
- UniProtKB: D3ZPP3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233654   ⟸   XM_006233592
- Peptide Label: isoform X1
- UniProtKB: D3ZPP3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233653   ⟸   XM_006233591
- Peptide Label: isoform X1
- UniProtKB: D3ZPP3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233655   ⟸   XM_006233593
- Peptide Label: isoform X2
- UniProtKB: A0A8I6A7Y6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008161   ⟸   ENSRNOT00000008161
RefSeq Acc Id: XP_038961105   ⟸   XM_039105177
- Peptide Label: isoform X1
- UniProtKB: D3ZPP3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961106   ⟸   XM_039105178
- Peptide Label: isoform X1
- UniProtKB: D3ZPP3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961107   ⟸   XM_039105179
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038961108   ⟸   XM_039105180
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000087791   ⟸   ENSRNOT00000099515
RefSeq Acc Id: XP_063139985   ⟸   XM_063283915
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063139986   ⟸   XM_063283916
- Peptide Label: isoform X5
Protein Domains
PH   SEC7

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZPP3-F1-model_v2 AlphaFold D3ZPP3 1-1007 view protein structure

Transcriptome

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

Promoters
RGD ID:13691849
Promoter ID:EPDNEW_R2374
Type:multiple initiation site
Name:Psd4_1
Description:pleckstrin and Sec7 domain containing 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_6.031,478,441 - 1,478,501EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310289 AgrOrtholog
BioCyc Gene G2FUF-50506 BioCyc
Ensembl Genes ENSRNOG00000006079 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008161 ENTREZGENE
  ENSRNOT00000008161.5 UniProtKB/TrEMBL
  ENSRNOT00000099515.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1000.11 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
InterPro PH_9 UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  Sec7 UniProtKB/TrEMBL
  SEC7_alpha_orthog UniProtKB/TrEMBL
  Sec7_sf UniProtKB/TrEMBL
  Spectrin_PH UniProtKB/TrEMBL
KEGG Report rno:311785 UniProtKB/TrEMBL
NCBI Gene 311785 ENTREZGENE
PANTHER GUANYL-NUCLEOTIDE EXCHANGE FACTOR UniProtKB/TrEMBL
  PH AND SEC7 DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
Pfam PH_9 UniProtKB/TrEMBL
  Sec7 UniProtKB/TrEMBL
PhenoGen Psd4 PhenoGen
PRINTS SPECTRINPH UniProtKB/TrEMBL
PROSITE PH_DOMAIN UniProtKB/TrEMBL
  SEC7 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006079 RatGTEx
SMART Sec7 UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP PH domain-like UniProtKB/TrEMBL
  Sec7 UniProtKB/TrEMBL
UniProt A0A8I6A7Y6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZPP3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Psd4  pleckstrin and Sec7 domain containing 4  Psd4_predicted  pleckstrin and Sec7 domain containing 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Psd4_predicted  pleckstrin and Sec7 domain containing 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED