Sgcg (sarcoglycan, gamma) - Rat Genome Database

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Gene: Sgcg (sarcoglycan, gamma) Rattus norvegicus
Analyze
Symbol: Sgcg
Name: sarcoglycan, gamma
RGD ID: 1359577
Description: Predicted to be involved in cardiac muscle tissue development and heart contraction. Predicted to act upstream of or within gene expression. Predicted to be located in plasma membrane. Predicted to be part of sarcoglycan complex. Predicted to be active in sarcolemma. Human ortholog(s) of this gene implicated in autosomal recessive limb-girdle muscular dystrophy type 2C and type 2 diabetes mellitus. Orthologous to human SGCG (sarcoglycan gamma); PARTICIPATES IN arrhythmogenic right ventricular cardiomyopathy pathway; dilated cardiomyopathy pathway; hypertrophic cardiomyopathy pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: gamma sarcoglycan; gamma-sarcoglycan; MGC94674; sarcoglycan, gamma (dystrophin-associated glycoprotein)
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
GRCr81539,564,920 - 39,611,149 (-)NCBIGRCr8
mRatBN7.21535,388,836 - 35,435,072 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1535,386,534 - 35,435,148 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1537,247,345 - 37,293,820 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01538,397,984 - 38,444,459 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01536,849,534 - 36,895,767 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01541,549,330 - 41,595,275 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1541,549,331 - 41,595,345 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01545,357,059 - 45,401,752 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41540,363,607 - 40,410,061 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11540,379,307 - 40,425,761 (-)NCBI
Celera1535,086,619 - 35,133,591 (-)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. A slowly progressive form of limb-girdle muscular dystrophy type 2C associated with founder mutation in the SGCG gene in Puerto Rican Hispanics. Al-Zaidy SA, etal., Mol Genet Genomic Med. 2015 Mar;3(2):92-8. doi: 10.1002/mgg3.125. Epub 2015 Jan 8.
2. Three single nucleotide polymorphisms associated with type 2 diabetes mellitus in a Chinese population. Chen M, etal., Exp Ther Med. 2017 Jan;13(1):121-126. doi: 10.3892/etm.2016.3920. Epub 2016 Nov 18.
3. 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.
4. Gamma-sarcoglycan deficiency leads to muscle membrane defects and apoptosis independent of dystrophin. Hack AA, etal., J Cell Biol 1998 Sep 7;142(5):1279-87.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. 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.
12. Novel mutations in three patients with LGMD2C with phenotypic differences. Vermeer S, etal., Pediatr Neurol. 2004 Apr;30(4):291-4.
Additional References at PubMed
PMID:10481911   PMID:10678176   PMID:12189167   PMID:16524571   PMID:17164264   PMID:22894000  


Genomics

Comparative Map Data
Sgcg
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81539,564,920 - 39,611,149 (-)NCBIGRCr8
mRatBN7.21535,388,836 - 35,435,072 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1535,386,534 - 35,435,148 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1537,247,345 - 37,293,820 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01538,397,984 - 38,444,459 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01536,849,534 - 36,895,767 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01541,549,330 - 41,595,275 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1541,549,331 - 41,595,345 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01545,357,059 - 45,401,752 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41540,363,607 - 40,410,061 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11540,379,307 - 40,425,761 (-)NCBI
Celera1535,086,619 - 35,133,591 (-)NCBICelera
Cytogenetic Map15p12NCBI
SGCG
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381323,160,508 - 23,325,162 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1323,180,979 - 23,325,162 (+)EnsemblGRCh38hg38GRCh38
GRCh371323,734,647 - 23,899,301 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361322,653,091 - 22,797,304 (+)NCBINCBI36Build 36hg18NCBI36
Build 341322,653,090 - 22,797,304NCBI
Celera134,818,082 - 4,962,307 (+)NCBICelera
Cytogenetic Map13q12.12NCBI
HuRef134,568,485 - 4,711,933 (+)NCBIHuRef
CHM1_11323,723,673 - 23,867,900 (+)NCBICHM1_1
T2T-CHM13v2.01322,367,302 - 22,531,974 (+)NCBIT2T-CHM13v2.0
Sgcg
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391461,456,555 - 61,495,939 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1461,456,564 - 61,495,939 (-)EnsemblGRCm39 Ensembl
GRCm381461,219,106 - 61,275,062 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1461,219,115 - 61,258,490 (-)EnsemblGRCm38mm10GRCm38
MGSCv371461,837,952 - 61,877,327 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361460,175,169 - 60,212,543 (-)NCBIMGSCv36mm8
MGSCv361452,317,272 - 52,354,896 (-)NCBIMGSCv36mm8
Celera1458,986,681 - 59,013,511 (-)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1432.27NCBI
Sgcg
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554973,615,003 - 3,701,300 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554973,592,041 - 3,702,780 (+)NCBIChiLan1.0ChiLan1.0
SGCG
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21422,775,506 - 22,942,534 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11313,882,542 - 14,049,284 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0134,471,680 - 4,638,419 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11322,767,914 - 22,932,350 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1322,810,771 - 22,932,350 (+)Ensemblpanpan1.1panPan2
SGCG
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12515,300,303 - 15,429,555 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2515,249,622 - 15,430,044 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2515,385,366 - 15,463,994 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02515,438,637 - 15,566,980 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2515,437,354 - 15,568,272 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12515,313,964 - 15,391,928 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02515,315,358 - 15,394,278 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02515,371,563 - 15,450,196 (-)NCBIUU_Cfam_GSD_1.0
Dog Cytomap25q21-q23NCBI
Sgcg
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945117,471,929 - 117,579,002 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366882,083,846 - 2,191,876 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366882,083,930 - 2,191,206 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SGCG
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1112,310,280 - 2,380,054 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2111,615,434 - 1,649,827 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SGCG
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.133,117,708 - 3,216,776 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl33,135,446 - 3,215,553 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605741,319,540 - 41,402,448 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sgcg
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477614,397,269 - 14,548,168 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477614,396,560 - 14,547,188 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sgcg
437 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:71
Count of miRNA genes:57
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000019639
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
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat

Markers in Region
RH137232  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21535,388,940 - 35,389,137 (+)MAPPERmRatBN7.2
Rnor_6.01541,549,435 - 41,549,631NCBIRnor6.0
Rnor_5.01545,357,164 - 45,357,360UniSTSRnor5.0
RGSC_v3.41540,363,712 - 40,363,908UniSTSRGSC3.4
Celera1535,086,724 - 35,086,920UniSTS
RH 3.4 Map15229.5UniSTS
Cytogenetic Map15p12UniSTS


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 29 3 2 8 11 3 6 8
Low 1 4 17 4 8 4 33 25 25 5
Below cutoff 2 8 11 11 9 11 9 10 13

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019639   ⟹   ENSRNOP00000019639
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1535,386,534 - 35,435,148 (-)Ensembl
Rnor_6.0 Ensembl1541,549,331 - 41,595,345 (-)Ensembl
RefSeq Acc Id: NM_001006993   ⟹   NP_001006994
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81539,564,920 - 39,611,149 (-)NCBI
mRatBN7.21535,388,836 - 35,435,072 (-)NCBI
Rnor_6.01541,549,330 - 41,595,275 (-)NCBI
Rnor_5.01545,357,059 - 45,401,752 (-)NCBI
RGSC_v3.41540,363,607 - 40,410,061 (-)RGD
Celera1535,086,619 - 35,133,591 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001006994 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83748 (Get FASTA)   NCBI Sequence Viewer  
  EDL85272 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019639
  ENSRNOP00000019639.4
Reference Protein Sequences
RefSeq Acc Id: NP_001006994   ⟸   NM_001006993
- UniProtKB: Q5XID6 (UniProtKB/TrEMBL),   A6K6B2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019639   ⟸   ENSRNOT00000019639

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XID6-F1-model_v2 AlphaFold Q5XID6 1-292 view protein structure

Transcriptome

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

Promoters
RGD ID:13699741
Promoter ID:EPDNEW_R10264
Type:initiation region
Name:Sgcg_1
Description:sarcoglycan, gamma
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_6.01541,595,295 - 41,595,355EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359577 AgrOrtholog
BioCyc Gene G2FUF-13512 BioCyc
Ensembl Genes ENSRNOG00000014603 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019639 ENTREZGENE
  ENSRNOT00000019639.6 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7192349 IMAGE-MGC_LOAD
InterPro Sarcoglycan UniProtKB/TrEMBL
  Sarcoglycan_gamma/delta/zeta UniProtKB/TrEMBL
KEGG Report rno:305941 UniProtKB/TrEMBL
MGC_CLONE MGC:94674 IMAGE-MGC_LOAD
NCBI Gene 305941 ENTREZGENE
PANTHER PTHR12939 UniProtKB/TrEMBL
  PTHR12939:SF4 UniProtKB/TrEMBL
Pfam Sarcoglycan_1 UniProtKB/TrEMBL
PhenoGen Sgcg PhenoGen
RatGTEx ENSRNOG00000014603 RatGTEx
UniProt A6K6B2 ENTREZGENE, UniProtKB/TrEMBL
  Q5XID6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-03-16 Sgcg  sarcoglycan, gamma  Sgcg  sarcoglycan, gamma (dystrophin-associated glycoprotein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Sgcg  sarcoglycan, gamma (dystrophin-associated glycoprotein)    gamma sarcoglycan  Name updated 1299863 APPROVED
2005-07-29 Sgcg  gamma sarcoglycan      Symbol and Name status set to provisional 70820 PROVISIONAL