Sntg1 (syntrophin, gamma 1) - Rat Genome Database

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Gene: Sntg1 (syntrophin, gamma 1) Rattus norvegicus
Analyze
Symbol: Sntg1
Name: syntrophin, gamma 1
RGD ID: 1560290
Description: Predicted to enable protein C-terminus binding activity. Predicted to be located in cytoplasm; cytoskeleton; and ruffle membrane. Predicted to be part of dystrophin-associated glycoprotein complex. Orthologous to human SNTG1 (syntrophin gamma 1); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: gamma-1-syntrophin; LOC102556371; LOC500394; RGD1560290; similar to syntrophin, gamma 1; uncharacterized LOC102556371
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
mRatBN7.259,980,550 - 10,794,666 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,981,115 - 10,791,181 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx512,570,179 - 12,939,304 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0514,218,411 - 14,604,829 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0513,904,867 - 14,274,007 (+)NCBIRnor_WKY
Rnor_6.0510,118,901 - 10,493,094 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl510,178,302 - 10,493,094 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0515,039,209 - 15,286,329 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4510,043,321 - 10,418,211 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera59,933,073 - 10,291,832 (+)NCBICelera
Cytogenetic Map5q11NCBI
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. GOA pipeline RGD automated data pipeline
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:15485858  


Genomics

Comparative Map Data
Sntg1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.259,980,550 - 10,794,666 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,981,115 - 10,791,181 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx512,570,179 - 12,939,304 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0514,218,411 - 14,604,829 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0513,904,867 - 14,274,007 (+)NCBIRnor_WKY
Rnor_6.0510,118,901 - 10,493,094 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl510,178,302 - 10,493,094 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0515,039,209 - 15,286,329 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4510,043,321 - 10,418,211 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera59,933,073 - 10,291,832 (+)NCBICelera
Cytogenetic Map5q11NCBI
SNTG1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38849,909,796 - 50,796,692 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl849,909,789 - 50,796,692 (+)EnsemblGRCh38hg38GRCh38
GRCh37850,822,356 - 51,709,252 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36850,987,150 - 51,867,980 (+)NCBINCBI36Build 36hg18NCBI36
Build 34850,987,149 - 51,867,980NCBI
Celera846,812,529 - 47,693,284 (+)NCBICelera
Cytogenetic Map8q11.21NCBI
HuRef846,289,537 - 47,171,268 (+)NCBIHuRef
CHM1_1850,876,886 - 51,757,725 (+)NCBICHM1_1
T2T-CHM13v2.0850,290,789 - 51,170,264 (+)NCBIT2T-CHM13v2.0
Sntg1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3918,429,963 - 9,371,882 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl18,431,699 - 9,370,103 (-)EnsemblGRCm39 Ensembl
GRCm3818,359,739 - 9,301,657 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl18,361,475 - 9,299,878 (-)EnsemblGRCm38mm10GRCm38
MGSCv3718,352,742 - 9,289,811 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3618,352,595 - 9,284,452 (-)NCBIMGSCv36mm8
Celera18,319,644 - 9,265,611 (-)NCBICelera
Cytogenetic Map1A1- A2NCBI
Sntg1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545410,174,380 - 10,439,874 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554549,698,609 - 10,439,874 (+)NCBIChiLan1.0ChiLan1.0
SNTG1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1843,750,466 - 44,607,233 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl844,214,273 - 44,606,891 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0846,358,675 - 47,223,131 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SNTG1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1292,000,167 - 2,819,468 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl292,522,653 - 2,818,410 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha292,427,062 - 3,256,355 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0292,056,582 - 2,879,126 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl292,478,892 - 2,879,277 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1291,998,582 - 2,812,831 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0292,225,602 - 3,043,266 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0292,298,045 - 3,111,263 (+)NCBIUU_Cfam_GSD_1.0
Sntg1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530376,816,902 - 77,613,904 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365902,003,351 - 2,562,850 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365902,006,927 - 2,803,088 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNTG1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl478,527,519 - 78,981,003 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1478,527,486 - 78,982,116 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SNTG1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1845,981,435 - 46,858,135 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603995,199,087 - 96,108,935 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sntg1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247354,758,511 - 5,063,007 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247354,757,825 - 5,647,328 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sntg1
4967 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:48
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000009679
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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat

Markers in Region
BE106282  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2510,503,823 - 10,504,043 (+)MAPPERmRatBN7.2
Rnor_6.0510,193,026 - 10,193,245NCBIRnor6.0
Rnor_5.0514,992,371 - 14,992,590UniSTSRnor5.0
RGSC_v3.4510,115,653 - 10,115,872UniSTSRGSC3.4
Celera510,003,865 - 10,004,084UniSTS
RH 3.4 Map549.3UniSTS
Cytogenetic Map5q11UniSTS
RH140340  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2510,790,961 - 10,791,122 (+)MAPPERmRatBN7.2
Rnor_6.0510,493,158 - 10,493,318NCBIRnor6.0
Rnor_5.0515,286,393 - 15,286,553UniSTSRnor5.0
RGSC_v3.4510,418,275 - 10,418,435UniSTSRGSC3.4
Celera510,291,896 - 10,292,056UniSTS
RH 3.4 Map552.3UniSTS
Cytogenetic Map5q11UniSTS


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 33
Low 1 2 2 2 35 22 26
Below cutoff 1 22 14 5 9 5 3 3 6 7 8 2 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009679   ⟹   ENSRNOP00000009679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl510,431,884 - 10,791,181 (+)Ensembl
Rnor_6.0 Ensembl510,178,302 - 10,493,094 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095256   ⟹   ENSRNOP00000081625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl59,981,115 - 10,791,181 (+)Ensembl
RefSeq Acc Id: NM_001191981   ⟹   NP_001178910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2510,431,884 - 10,790,898 (+)NCBI
Rnor_6.0510,118,901 - 10,493,094 (+)NCBI
Rnor_5.0515,039,209 - 15,286,329 (+)NCBI
Celera59,933,073 - 10,291,832 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039110525   ⟹   XP_038966453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2510,153,801 - 10,794,666 (+)NCBI
RefSeq Acc Id: XM_039110526   ⟹   XP_038966454
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,980,551 - 10,794,666 (+)NCBI
RefSeq Acc Id: XM_039110527   ⟹   XP_038966455
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2510,153,799 - 10,794,666 (+)NCBI
RefSeq Acc Id: XM_039110528   ⟹   XP_038966456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.259,980,550 - 10,794,666 (+)NCBI
RefSeq Acc Id: XM_039110529   ⟹   XP_038966457
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2510,153,799 - 10,794,666 (+)NCBI
RefSeq Acc Id: XM_039110530   ⟹   XP_038966458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2510,153,788 - 10,794,666 (+)NCBI
RefSeq Acc Id: XM_039110531   ⟹   XP_038966459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2510,490,355 - 10,794,666 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178910   ⟸   NM_001191981
- Sequence:
RefSeq Acc Id: ENSRNOP00000009679   ⟸   ENSRNOT00000009679
RefSeq Acc Id: XP_038966456   ⟸   XM_039110528
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZSX2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966454   ⟸   XM_039110526
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038966458   ⟸   XM_039110530
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966455   ⟸   XM_039110527
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZSX2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966457   ⟸   XM_039110529
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZSX2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966453   ⟸   XM_039110525
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZSX2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966459   ⟸   XM_039110531
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000081625   ⟸   ENSRNOT00000095256
Protein Domains
PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M2M1-F1-model_v2 AlphaFold F1M2M1 1-426 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560290 AgrOrtholog
BioCyc Gene G2FUF-42193 BioCyc
Ensembl Genes ENSRNOG00000007294 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009679.8 UniProtKB/TrEMBL
  ENSRNOP00000081625 ENTREZGENE
  ENSRNOP00000081625.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009679.8 UniProtKB/TrEMBL
  ENSRNOT00000095256 ENTREZGENE
  ENSRNOT00000095256.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
  2.30.42.10 UniProtKB/TrEMBL
InterPro PDZ UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  PH_dom-like UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  Syntrophin UniProtKB/TrEMBL
  Syntrophin_gamma UniProtKB/TrEMBL
NCBI Gene 500394 ENTREZGENE
PANTHER PTHR10554 UniProtKB/TrEMBL
  PTHR10554:SF2 UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
PhenoGen Sntg1 PhenoGen
PROSITE PDZ UniProtKB/TrEMBL
SMART PDZ UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/TrEMBL
UniProt A0A8I5ZSX2 ENTREZGENE, UniProtKB/TrEMBL
  F1M2M1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Sntg1  syntrophin, gamma 1  LOC102556371  uncharacterized LOC102556371  Data Merged 737654 PROVISIONAL
2013-12-18 LOC102556371  uncharacterized LOC102556371      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-02-28 Sntg1  syntrophin, gamma 1  RGD1560290_predicted  similar to syntrophin, gamma 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560290_predicted  similar to syntrophin, gamma 1 (predicted)  LOC500394  similar to syntrophin, gamma 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500394  similar to syntrophin, gamma 1      Symbol and Name status set to provisional 70820 PROVISIONAL