SGCD (sarcoglycan delta) - Rat Genome Database

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Gene: SGCD (sarcoglycan delta) Canis lupus familiaris
Analyze
Symbol: SGCD
Name: sarcoglycan delta
RGD ID: 12140215
Description: INVOLVED IN calcium ion homeostasis (ortholog); calcium-mediated signaling (ortholog); cardiac muscle cell contraction (ortholog); ASSOCIATED WITH autosomal recessive limb-girdle muscular dystrophy type 2F; autosomal recessive limb-girdle muscular dystrophy (ortholog); cardiomyopathy (ortholog); FOUND IN cytoskeleton (inferred); dystroglycan complex (inferred); dystrophin-associated glycoprotein complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: delta-sarcoglycan
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1453,259,332 - 54,178,228 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl453,263,866 - 53,820,231 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha453,151,553 - 54,062,671 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0453,696,389 - 54,612,269 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl453,701,146 - 54,093,152 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1453,521,774 - 54,443,521 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0453,631,480 - 54,544,178 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0454,146,275 - 55,057,219 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:28697784   PMID:30032202  


Genomics

Comparative Map Data
SGCD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1453,259,332 - 54,178,228 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl453,263,866 - 53,820,231 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha453,151,553 - 54,062,671 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0453,696,389 - 54,612,269 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl453,701,146 - 54,093,152 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1453,521,774 - 54,443,521 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0453,631,480 - 54,544,178 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0454,146,275 - 55,057,219 (-)NCBIUU_Cfam_GSD_1.0
SGCD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385155,727,832 - 156,767,788 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5155,870,344 - 156,767,788 (+)EnsemblGRCh38hg38GRCh38
GRCh375155,754,174 - 156,194,799 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365155,686,345 - 156,125,639 (+)NCBINCBI36Build 36hg18NCBI36
Build 345155,686,344 - 156,117,646NCBI
Celera5151,779,805 - 152,220,524 (+)NCBICelera
Cytogenetic Map5q33.2-q33.3NCBI
HuRef5150,847,340 - 151,288,441 (+)NCBIHuRef
CHM1_15155,186,188 - 155,627,222 (+)NCBICHM1_1
T2T-CHM13v2.05156,261,684 - 157,286,763 (+)NCBIT2T-CHM13v2.0
Sgcd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391146,861,904 - 47,880,309 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1146,787,080 - 47,879,796 (-)EnsemblGRCm39 Ensembl
GRCm381146,971,077 - 47,989,451 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1146,896,253 - 47,988,969 (-)EnsemblGRCm38mm10GRCm38
MGSCv371146,792,285 - 47,192,804 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361146,822,206 - 47,222,725 (-)NCBIMGSCv36mm8
Celera1151,565,425 - 51,970,242 (-)NCBICelera
Cytogenetic Map11B1.1NCBI
Sgcd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81031,847,713 - 32,829,554 (-)NCBIGRCr8
mRatBN7.21031,346,480 - 32,328,364 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1031,280,511 - 31,724,840 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1036,077,225 - 36,471,243 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0104,615,625 - 5,009,663 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01031,062,074 - 31,463,752 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01032,062,946 - 32,471,454 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1032,062,946 - 32,471,454 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01031,878,904 - 32,285,036 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41032,084,678 - 32,489,330 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1030,793,915 - 31,190,298 (-)NCBICelera
Cytogenetic Map10q21NCBI
Sgcd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540810,273,223 - 10,819,072 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540810,273,344 - 10,820,108 (+)NCBIChiLan1.0ChiLan1.0
SGCD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24150,925,175 - 151,958,431 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15149,065,868 - 150,104,107 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05151,131,909 - 152,164,077 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15157,119,158 - 158,148,016 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5157,719,540 - 158,139,633 (+)Ensemblpanpan1.1panPan2
Sgcd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213107,825,301 - 108,458,847 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365156,283,051 - 6,908,174 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365156,278,631 - 6,908,193 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SGCD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1666,452,178 - 66,887,924 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11666,447,982 - 67,481,709 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21672,423,126 - 72,526,427 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SGCD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12358,095,013 - 59,177,752 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603418,457,325 - 19,501,690 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sgcd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473332,663,025 - 33,080,608 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473332,654,754 - 33,626,227 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SGCD
12021 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 5 6 4 1
Low 4 19 6 6 6 6 12 8 4 5
Below cutoff 1 3 2

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005619257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_014113050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_014113051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022417768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038473841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038473842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038473843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038534930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038534931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038534932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038599230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038599231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038599232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038663534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038663535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038663536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000027892   ⟹   ENSCAFP00000025939
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl453,267,638 - 53,820,231 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000082584   ⟹   ENSCAFP00000044826
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl453,263,866 - 53,665,366 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845004571   ⟹   ENSCAFP00845003652
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl453,701,146 - 54,053,162 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845004582   ⟹   ENSCAFP00845003660
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl453,702,112 - 54,093,152 (-)Ensembl
RefSeq Acc Id: XM_005619257   ⟹   XP_005619314
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1453,259,332 - 53,642,677 (-)NCBI
Dog10K_Boxer_Tasha453,151,553 - 53,528,087 (-)NCBI
Sequence:
RefSeq Acc Id: XM_014113050   ⟹   XP_013968525
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1453,259,332 - 54,178,228 (-)NCBI
Dog10K_Boxer_Tasha453,151,553 - 54,062,671 (-)NCBI
Sequence:
RefSeq Acc Id: XM_014113051   ⟹   XP_013968526
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1453,259,332 - 53,643,023 (-)NCBI
Dog10K_Boxer_Tasha453,151,553 - 53,528,454 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038473841   ⟹   XP_038329769
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1453,521,774 - 53,904,300 (-)NCBI
RefSeq Acc Id: XM_038473842   ⟹   XP_038329770
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1453,521,774 - 54,443,521 (-)NCBI
RefSeq Acc Id: XM_038473843   ⟹   XP_038329771
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1453,521,774 - 53,904,667 (-)NCBI
RefSeq Acc Id: XM_038534930   ⟹   XP_038390858
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0454,146,275 - 54,523,074 (-)NCBI
RefSeq Acc Id: XM_038534931   ⟹   XP_038390859
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0454,146,275 - 55,057,219 (-)NCBI
RefSeq Acc Id: XM_038534932   ⟹   XP_038390860
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0454,146,275 - 54,523,441 (-)NCBI
RefSeq Acc Id: XM_038599230   ⟹   XP_038455158
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0453,631,480 - 54,009,189 (-)NCBI
RefSeq Acc Id: XM_038599231   ⟹   XP_038455159
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0453,631,480 - 54,544,178 (-)NCBI
RefSeq Acc Id: XM_038599232   ⟹   XP_038455160
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0453,631,480 - 54,009,556 (-)NCBI
RefSeq Acc Id: XM_038663534   ⟹   XP_038519462
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0453,696,389 - 54,070,395 (-)NCBI
RefSeq Acc Id: XM_038663535   ⟹   XP_038519463
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0453,696,389 - 54,612,269 (-)NCBI
RefSeq Acc Id: XM_038663536   ⟹   XP_038519464
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0453,696,389 - 54,070,762 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_013968525   ⟸   XM_014113050
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013968526   ⟸   XM_014113051
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005619314   ⟸   XM_005619257
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000025939   ⟸   ENSCAFT00000027892
RefSeq Acc Id: ENSCAFP00000044826   ⟸   ENSCAFT00000082584
RefSeq Acc Id: XP_038329770   ⟸   XM_038473842
RefSeq Acc Id: XP_038329771   ⟸   XM_038473843
RefSeq Acc Id: XP_038329769   ⟸   XM_038473841
RefSeq Acc Id: XP_038455159   ⟸   XM_038599231
RefSeq Acc Id: XP_038455160   ⟸   XM_038599232
RefSeq Acc Id: XP_038455158   ⟸   XM_038599230
RefSeq Acc Id: XP_038519463   ⟸   XM_038663535
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038519464   ⟸   XM_038663536
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038519462   ⟸   XM_038663534
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038390859   ⟸   XM_038534931
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038390860   ⟸   XM_038534932
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038390858   ⟸   XM_038534930
- UniProtKB: A0A8C0MWE3 (UniProtKB/TrEMBL),   A0A8I3N2L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845003660   ⟸   ENSCAFT00845004582
RefSeq Acc Id: ENSCAFP00845003652   ⟸   ENSCAFT00845004571

Promoters
RGD ID:13683008
Promoter ID:EPDNEW_C1075
Type:initiation region
Name:SGCD_1
Description:sarcoglycan delta
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1453,642,454 - 53,642,514EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000017592 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030009502 UniProtKB/TrEMBL
  ENSCAFG00040005936 UniProtKB/TrEMBL
  ENSCAFG00845002587 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000027892.5 UniProtKB/TrEMBL
  ENSCAFT00000082584.2 UniProtKB/TrEMBL
  ENSCAFT00030017693.1 UniProtKB/TrEMBL
  ENSCAFT00040011090.1 UniProtKB/TrEMBL
  ENSCAFT00845004571.1 UniProtKB/TrEMBL
  ENSCAFT00845004582 ENTREZGENE
  ENSCAFT00845004582.1 UniProtKB/TrEMBL
InterPro Sarcoglycan UniProtKB/TrEMBL
  Sarcoglycan_gamma/delta/zeta UniProtKB/TrEMBL
NCBI Gene SGCD ENTREZGENE
PANTHER PTHR12939 UniProtKB/TrEMBL
  PTHR12939:SF6 UniProtKB/TrEMBL
Pfam Sarcoglycan_1 UniProtKB/TrEMBL
UniProt A0A8C0MWE3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3MLE0_CANLF UniProtKB/TrEMBL
  A0A8I3N2L6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0NIW2_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:46093 ENTREZGENE