Dsc1 (desmocollin 1) - Rat Genome Database

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Gene: Dsc1 (desmocollin 1) Rattus norvegicus
Analyze
Symbol: Dsc1
Name: desmocollin 1
RGD ID: 1310768
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to be located in desmosome. Orthologous to human DSC1 (desmocollin 1); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: desmocollin-1; LOC102555477; LOC291759; uncharacterized LOC102555477
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
GRCr81811,774,711 - 11,831,868 (-)NCBIGRCr8
mRatBN7.21811,499,936 - 11,556,801 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1811,502,003 - 11,528,494 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01811,877,918 - 11,906,828 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1811,877,561 - 11,906,827 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01811,677,463 - 11,706,220 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41811,953,172 - 11,979,048 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11811,980,205 - 12,050,014 (-)NCBI
Celera1811,519,677 - 11,545,279 (-)NCBICelera
Cytogenetic Map18p12NCBI
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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Altered gene expression in leukocyte transendothelial migration and cell communication pathways in periodontitis-affected gingival tissues. Abe D, etal., J Periodontal Res. 2011 Jun;46(3):345-53. doi: 10.1111/j.1600-0765.2011.01349.x. Epub 2011 Mar 7.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14673151   PMID:23376485   PMID:23533145  


Genomics

Comparative Map Data
Dsc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81811,774,711 - 11,831,868 (-)NCBIGRCr8
mRatBN7.21811,499,936 - 11,556,801 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1811,502,003 - 11,528,494 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01811,877,918 - 11,906,828 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1811,877,561 - 11,906,827 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01811,677,463 - 11,706,220 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41811,953,172 - 11,979,048 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11811,980,205 - 12,050,014 (-)NCBI
Celera1811,519,677 - 11,545,279 (-)NCBICelera
Cytogenetic Map18p12NCBI
DSC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381831,129,236 - 31,162,856 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1831,129,236 - 31,162,856 (-)EnsemblGRCh38hg38GRCh38
GRCh371828,709,199 - 28,742,819 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361826,963,197 - 26,996,817 (-)NCBINCBI36Build 36hg18NCBI36
Build 341826,963,213 - 26,996,817NCBI
Celera1825,517,395 - 25,550,695 (-)NCBICelera
Cytogenetic Map18q12.1ENTREZGENE
HuRef1825,564,926 - 25,598,451 (-)NCBIHuRef
CHM1_11828,636,224 - 28,670,180 (-)NCBICHM1_1
T2T-CHM13v2.01831,319,561 - 31,418,220 (-)NCBIT2T-CHM13v2.0
Dsc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391820,216,528 - 20,247,830 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1820,217,241 - 20,247,928 (-)EnsemblGRCm39 Ensembl
GRCm381820,083,471 - 20,114,773 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1820,084,184 - 20,114,871 (-)EnsemblGRCm38mm10GRCm38
MGSCv371820,243,204 - 20,273,274 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361820,228,175 - 20,257,690 (-)NCBIMGSCv36mm8
Celera1820,586,914 - 20,616,991 (-)NCBICelera
Cytogenetic Map18A2NCBI
cM Map1811.17NCBI
Dsc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540218,513,817 - 18,543,720 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540218,514,657 - 18,543,449 (-)NCBIChiLan1.0ChiLan1.0
DSC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21748,532,785 - 48,568,696 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11834,225,380 - 34,261,291 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01824,358,116 - 24,393,604 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11827,957,559 - 27,990,818 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1827,955,717 - 27,990,818 (-)Ensemblpanpan1.1panPan2
DSC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1758,322,959 - 58,350,092 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl758,322,959 - 58,457,978 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha757,760,078 - 57,787,216 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0758,308,188 - 58,335,350 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl758,308,188 - 58,387,461 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1757,984,457 - 58,011,580 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0758,009,130 - 58,036,271 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0758,299,991 - 58,327,147 (+)NCBIUU_Cfam_GSD_1.0
Dsc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494454,011,718 - 54,039,448 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366822,013,414 - 2,040,148 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366822,013,414 - 2,040,148 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DSC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6115,039,722 - 115,076,097 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16115,042,225 - 115,076,097 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26107,662,809 - 107,696,605 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DSC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11849,547,141 - 49,578,226 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1849,549,287 - 49,576,545 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605024,194,322 - 24,223,576 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Dsc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247701,710,170 - 1,740,454 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247701,709,920 - 1,743,005 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Dsc1
428 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125758124Rat
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125758124Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor surface area measurement (CMO:0002078)18224947722066430Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)18224947722066430Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
11565454Kidm59Kidney mass QTL 590.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)18679125112205285Rat
12904714Cm131Cardiac mass QTL 1310.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)18679125112205285Rat
12904715Cm132Cardiac mass QTL 1320.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)18679125112205285Rat
12904716Am21Aortic mass QTL 210.005aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)18679125112205285Rat
2301409Cm70Cardiac mass QTL 700.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)18679125112205285Rat

Markers in Region
X97986  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21811,502,830 - 11,502,964 (+)MAPPERmRatBN7.2
Rnor_6.01811,878,377 - 11,878,510NCBIRnor6.0
Rnor_5.01811,677,922 - 11,678,055UniSTSRnor5.0
RGSC_v3.41811,953,621 - 11,953,754UniSTSRGSC3.4
Celera1811,520,136 - 11,520,269UniSTS
Cytogenetic Map18p12UniSTS


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

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 5
Low 1 1 11 2 1
Below cutoff 13 13 4 10 4 2 2 32 6 15 2 2

Sequence


RefSeq Acc Id: ENSRNOT00000078207   ⟹   ENSRNOP00000075307
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1811,502,003 - 11,528,494 (-)Ensembl
Rnor_6.0 Ensembl1811,877,561 - 11,906,827 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118489   ⟹   ENSRNOP00000085728
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1811,502,747 - 11,528,494 (-)Ensembl
RefSeq Acc Id: NM_001106161   ⟹   NP_001099631
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81811,775,010 - 11,803,522 (-)NCBI
RefSeq Acc Id: XM_039097286   ⟹   XP_038953214
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81811,774,711 - 11,831,868 (-)NCBI
mRatBN7.21811,499,936 - 11,556,801 (-)NCBI
RefSeq Acc Id: XM_039097287   ⟹   XP_038953215
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81811,774,711 - 11,831,868 (-)NCBI
mRatBN7.21811,499,936 - 11,556,801 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099631 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953214 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953215 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76086 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000075307.2
  ENSRNOP00000085728.1
RefSeq Acc Id: ENSRNOP00000075307   ⟸   ENSRNOT00000078207
RefSeq Acc Id: XP_038953215   ⟸   XM_039097287
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GE75 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038953214   ⟸   XM_039097286
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GE75 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000085728   ⟸   ENSRNOT00000118489
RefSeq Acc Id: NP_001099631   ⟸   NM_001106161
- Peptide Label: precursor
- UniProtKB: A0A8I6GE75 (UniProtKB/TrEMBL)
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KA90-F1-model_v2 AlphaFold A0A0G2KA90 1-843 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:1310768 AgrOrtholog
BioCyc Gene G2FUF-8238 BioCyc
Ensembl Genes ENSRNOG00000056258 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078207.2 UniProtKB/TrEMBL
  ENSRNOT00000118489.1 UniProtKB/TrEMBL
Gene3D-CATH 4.10.900.10 UniProtKB/TrEMBL
  Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_cytoplasmic-dom UniProtKB/TrEMBL
  Cadherin_pro_dom UniProtKB/TrEMBL
  Catenin-bd_sf UniProtKB/TrEMBL
  Desmosomal_cadherin UniProtKB/TrEMBL
NCBI Gene 291759 ENTREZGENE
PANTHER CADHERIN-13 UniProtKB/TrEMBL
  CADHERIN-23 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_pro UniProtKB/TrEMBL
PhenoGen Dsc1 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
  DESMOCADHERN UniProtKB/TrEMBL
  DESMOCOLLIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000056258 RatGTEx
SMART Cadherin_pro UniProtKB/TrEMBL
  SM00112 UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/TrEMBL
UniProt A0A0G2KA90_RAT UniProtKB/TrEMBL
  A0A8I6GE75 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Dsc1  desmocollin 1  LOC102555477  uncharacterized LOC102555477  Data merged from RGD:7605114 737654 PROVISIONAL
2013-12-18 LOC102555477  uncharacterized LOC102555477      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Dsc1  desmocollin 1   Dsc1_predicted  desmocollin 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Dsc1_predicted  desmocollin 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED