Stpg3 (sperm-tail PG-rich repeat containing 3) - Rat Genome Database

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Gene: Stpg3 (sperm-tail PG-rich repeat containing 3) Rattus norvegicus
Analyze
Symbol: Stpg3
Name: sperm-tail PG-rich repeat containing 3
RGD ID: 1561978
Description: Predicted to be active in cytoskeleton. Orthologous to human STPG3 (sperm-tail PG-rich repeat containing 3); INTERACTS WITH bisphenol A; Cuprizon; gentamycin.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BC033939; hypothetical protein LOC499746; LOC499746; similar to hypothetical gene supported by AK097565; uncharacterized protein C9orf173 homolog; uncharacterized protein LOC499746
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
mRatBN7.238,028,122 - 8,030,546 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,028,131 - 8,034,601 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,132,811 - 11,135,220 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0319,719,040 - 19,721,449 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0317,908,883 - 17,911,292 (-)NCBIRnor_WKY
Rnor_6.032,431,757 - 2,434,258 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,432,690 - 2,434,257 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,413,055 - 2,415,557 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,378,151 - 3,379,718 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera32,854,726 - 2,857,227 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoskeleton  (IBA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data
Stpg3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.238,028,122 - 8,030,546 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,028,131 - 8,034,601 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,132,811 - 11,135,220 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0319,719,040 - 19,721,449 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0317,908,883 - 17,911,292 (-)NCBIRnor_WKY
Rnor_6.032,431,757 - 2,434,258 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,432,690 - 2,434,257 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,413,055 - 2,415,557 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,378,151 - 3,379,718 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera32,854,726 - 2,857,227 (-)NCBICelera
Cytogenetic Map3p13NCBI
STPG3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389137,251,286 - 137,253,483 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl9137,251,261 - 137,253,483 (+)EnsemblGRCh38hg38GRCh38
GRCh379140,145,738 - 140,147,935 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,265,551 - 139,267,755 (+)NCBINCBI36Build 36hg18NCBI36
Celera9110,661,314 - 110,663,520 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,605,025 - 109,607,249 (+)NCBIHuRef
CHM1_19140,294,447 - 140,296,669 (+)NCBICHM1_1
T2T-CHM13v2.09149,488,954 - 149,491,153 (+)NCBIT2T-CHM13v2.0
Stpg3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,102,219 - 25,108,719 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,102,219 - 25,104,649 (-)EnsemblGRCm39 Ensembl
GRCm38225,212,207 - 25,218,707 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,212,207 - 25,214,637 (-)EnsemblGRCm38mm10GRCm38
MGSCv37225,068,079 - 25,070,150 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,034,216 - 25,036,640 (-)NCBIMGSCv36mm8
Celera224,940,334 - 24,942,405 (-)NCBICelera
Cytogenetic Map2A3NCBI
Stpg3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,245,861 - 5,247,582 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,245,861 - 5,247,582 (+)NCBIChiLan1.0ChiLan1.0
STPG3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19137,278,739 - 137,282,670 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,278,844 - 137,282,670 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09108,310,511 - 108,314,233 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
STPG3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,424,901 - 48,426,814 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,609,375 - 47,613,145 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,284,231 - 49,287,977 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,286,196 - 49,287,912 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,060,637 - 48,064,383 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,361,423 - 48,363,207 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,406,345 - 48,410,142 (-)NCBIUU_Cfam_GSD_1.0
Stpg3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,632,392 - 202,634,287 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936669740,694 - 742,142 (-)EnsemblSpeTri2.0
SpeTri2.0NW_004936669740,953 - 742,571 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
STPG3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21314,128,289 - 314,129,751 (-)NCBISscrofa10.2Sscrofa10.2susScr3
STPG3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112934,282 - 937,697 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660584,370,359 - 4,372,686 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Stpg3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624760705,486 - 706,898 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624760703,733 - 707,880 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Stpg3
4 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:80
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000013278
Prediction methods:Microtar, 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
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


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 7
Low 8 4 5 4 1 3 23 4 1 1
Below cutoff 2 24 30 19 14 19 6 7 49 23 20 10 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001399436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_001077344 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233650 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_575081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005502049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC082090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC100078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC160838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000013278   ⟹   ENSRNOP00000013278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,028,131 - 8,034,601 (-)Ensembl
Rnor_6.0 Ensembl32,432,690 - 2,434,257 (-)Ensembl
RefSeq Acc Id: XM_006233649   ⟹   XP_006233711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,028,122 - 8,030,546 (-)NCBI
Rnor_6.032,431,870 - 2,434,258 (-)NCBI
Rnor_5.032,413,055 - 2,415,557 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233650   ⟹   XP_006233712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,028,122 - 8,030,546 (-)NCBI
Rnor_6.032,431,757 - 2,434,258 (-)NCBI
Rnor_5.032,413,055 - 2,415,557 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039106114   ⟹   XP_038962042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,028,122 - 8,030,546 (-)NCBI
RefSeq Acc Id: XM_039106115   ⟹   XP_038962043
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,028,122 - 8,030,518 (-)NCBI
RefSeq Acc Id: XM_575081   ⟹   XP_575081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,028,122 - 8,030,546 (-)NCBI
Rnor_6.032,431,757 - 2,434,258 (-)NCBI
Rnor_5.032,413,055 - 2,415,557 (-)NCBI
RGSC_v3.433,378,151 - 3,379,718 (-)RGD
Sequence:
RefSeq Acc Id: XR_005502049
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,028,122 - 8,030,546 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_575081   ⟸   XM_575081
- Peptide Label: isoform X3
- UniProtKB: D3ZRE5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233712   ⟸   XM_006233650
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006233711   ⟸   XM_006233649
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000013278   ⟸   ENSRNOT00000013278
RefSeq Acc Id: XP_038962042   ⟸   XM_039106114
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038962043   ⟸   XM_039106115
- Peptide Label: isoform X5

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRE5-F1-model_v2 AlphaFold D3ZRE5 1-305 view protein structure

Transcriptome

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

Promoters
RGD ID:13691868
Promoter ID:EPDNEW_R2385
Type:multiple initiation site
Name:Stpg3_1
Description:sperm-tail PG-rich repeat containing 3
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_6.032,434,244 - 2,434,304EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561978 AgrOrtholog
BioCyc Gene G2FUF-50478 BioCyc
Ensembl Genes ENSRNOG00000010002 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013278 ENTREZGENE
  ENSRNOP00000013278.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013278 ENTREZGENE
  ENSRNOT00000013278.6 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7132193 IMAGE-MGC_LOAD
InterPro SHIPPO-rpt UniProtKB/TrEMBL
MGC_CLONE MGC:112696 IMAGE-MGC_LOAD
NCBI Gene 499746 ENTREZGENE
Pfam SHIPPO-rpt UniProtKB/TrEMBL
PhenoGen Stpg3 PhenoGen
UniProt D3ZRE5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-27 Stpg3  sperm-tail PG-rich repeat containing 3  LOC499746  similar to hypothetical gene supported by AK097565; BC033939  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC499746  similar to hypothetical gene supported by AK097565; BC033939      Symbol and Name status set to provisional 70820 PROVISIONAL