SDC1 (syndecan 1) - Rat Genome Database

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Gene: SDC1 (syndecan 1) Sus scrofa
Analyze
Symbol: SDC1
Name: syndecan 1
RGD ID: 13964845
Description: ENCODES a protein that exhibits cargo receptor activity (inferred); identical protein binding (inferred); INVOLVED IN canonical Wnt signaling pathway (ortholog); response to calcium ion (ortholog); response to cAMP (ortholog); PARTICIPATES IN altered melanocortin system pathway; melanocortin system pathway; obesity pathway; ASSOCIATED WITH COVID-19 (ortholog); familial hyperlipidemia (ortholog); genetic disease (ortholog); FOUND IN plasma membrane (ortholog); protein-containing complex (ortholog); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: syndecan-1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3117,987,557 - 118,011,884 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13117,987,585 - 118,011,886 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23125,988,758 - 126,027,188 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:30032202   PMID:32575635  


Genomics

Comparative Map Data
SDC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3117,987,557 - 118,011,884 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13117,987,585 - 118,011,886 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23125,988,758 - 126,027,188 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38220,200,797 - 20,225,475 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl220,200,797 - 20,225,433 (-)EnsemblGRCh38hg38GRCh38
GRCh37220,400,558 - 20,425,236 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36220,264,039 - 20,288,675 (-)NCBINCBI36Build 36hg18NCBI36
Build 34220,322,187 - 20,346,555NCBI
Celera220,262,845 - 20,287,481 (-)NCBICelera
Cytogenetic Map2p24.1NCBI
HuRef220,158,155 - 20,182,491 (-)NCBIHuRef
CHM1_1220,329,922 - 20,354,554 (-)NCBICHM1_1
T2T-CHM13v2.0220,234,345 - 20,259,019 (-)NCBIT2T-CHM13v2.0
Sdc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39128,821,396 - 8,843,716 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl128,821,323 - 8,843,715 (+)EnsemblGRCm39 Ensembl
GRCm38128,771,396 - 8,793,716 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl128,771,323 - 8,793,715 (+)EnsemblGRCm38mm10GRCm38
MGSCv37128,778,202 - 8,800,494 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36128,797,404 - 8,819,696 (+)NCBIMGSCv36mm8
Celera129,156,353 - 9,178,644 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map123.94NCBI
Sdc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8637,282,041 - 37,304,503 (+)NCBIGRCr8
mRatBN7.2631,562,799 - 31,585,267 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl631,562,739 - 31,585,264 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx631,854,836 - 31,877,298 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0632,170,692 - 32,193,154 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0631,645,292 - 31,667,755 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0633,885,576 - 33,908,038 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl633,885,495 - 33,908,016 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0643,667,444 - 43,689,903 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4632,253,352 - 32,275,812 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1632,256,304 - 32,278,764 (+)NCBI
Celera631,009,934 - 31,032,396 (+)NCBICelera
Cytogenetic Map6q14NCBI
Sdc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554692,762,696 - 2,773,697 (-)NCBIChiLan1.0ChiLan1.0
SDC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212106,303,344 - 106,327,699 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A106,307,316 - 106,331,671 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A20,187,249 - 20,211,567 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A20,302,589 - 20,309,848 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A20,302,589 - 20,309,848 (-)Ensemblpanpan1.1panPan2
SDC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11715,220,906 - 15,243,974 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1715,222,094 - 15,243,890 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1715,185,971 - 15,208,368 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01715,373,622 - 15,395,937 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1715,373,628 - 15,395,946 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11715,227,151 - 15,249,524 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01715,233,919 - 15,256,296 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01715,265,578 - 15,287,885 (-)NCBIUU_Cfam_GSD_1.0
Sdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629259,639,887 - 59,661,785 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649311,177,708 - 11,199,804 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649311,177,804 - 11,199,678 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11487,499,732 - 87,523,122 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1487,499,574 - 87,525,026 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604524,701,281 - 24,725,764 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247382,920,154 - 2,938,035 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SDC1
835 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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 7 1 2 1 1
Low 3 2 3 4 4 2 2
Below cutoff 1 1 11

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000033465   ⟹   ENSSSCP00000029408
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl3117,987,557 - 118,011,879 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000055325   ⟹   ENSSSCP00000049762
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl3117,987,843 - 118,011,884 (+)Ensembl
RefSeq Acc Id: NM_001243190   ⟹   NP_001230119
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.13117,987,585 - 118,011,884 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021085689   ⟹   XP_020941348
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.13117,988,085 - 118,011,886 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001230119   ⟸   NM_001243190
- Peptide Label: precursor
- UniProtKB: K7GNF5 (UniProtKB/TrEMBL),   A0A4X1U4Q2 (UniProtKB/TrEMBL),   M5DFN4 (UniProtKB/TrEMBL),   A0A8D0Y314 (UniProtKB/TrEMBL),   A0A8D1K069 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020941348   ⟸   XM_021085689
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSSSCP00000049762   ⟸   ENSSSCT00000055325
RefSeq Acc Id: ENSSSCP00000029408   ⟸   ENSSSCT00000033465
Protein Domains
Neurexin/syndecan/glycophorin C


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000008601 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00025011513 UniProtKB/TrEMBL
  ENSSSCG00030067731 UniProtKB/TrEMBL
  ENSSSCG00035025436 UniProtKB/TrEMBL
  ENSSSCG00040010977 UniProtKB/TrEMBL
  ENSSSCG00045017212 UniProtKB/TrEMBL
  ENSSSCG00050073600 UniProtKB/TrEMBL
  ENSSSCG00055012204 UniProtKB/TrEMBL
  ENSSSCG00060032441 UniProtKB/TrEMBL
  ENSSSCG00065002804 UniProtKB/TrEMBL
  ENSSSCG00070014573 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000033465 ENTREZGENE
  ENSSSCT00000033465.4 UniProtKB/TrEMBL
  ENSSSCT00000055325.3 UniProtKB/TrEMBL
  ENSSSCT00025015113.1 UniProtKB/TrEMBL
  ENSSSCT00025015176.1 UniProtKB/TrEMBL
  ENSSSCT00030094789.1 UniProtKB/TrEMBL
  ENSSSCT00035033508.1 UniProtKB/TrEMBL
  ENSSSCT00035033524.1 UniProtKB/TrEMBL
  ENSSSCT00040014391.1 UniProtKB/TrEMBL
  ENSSSCT00045029311.1 UniProtKB/TrEMBL
  ENSSSCT00045029355.1 UniProtKB/TrEMBL
  ENSSSCT00050100664.1 UniProtKB/TrEMBL
  ENSSSCT00055023923.1 UniProtKB/TrEMBL
  ENSSSCT00055023952.1 UniProtKB/TrEMBL
  ENSSSCT00060043927.1 UniProtKB/TrEMBL
  ENSSSCT00065003634.1 UniProtKB/TrEMBL
  ENSSSCT00065003640.1 UniProtKB/TrEMBL
  ENSSSCT00070028581.1 UniProtKB/TrEMBL
InterPro Neurexin-like UniProtKB/TrEMBL
  Syndecan UniProtKB/TrEMBL
  Syndecan/Neurexin_dom UniProtKB/TrEMBL
  Syndecan_CS UniProtKB/TrEMBL
KEGG Report ssc:100519770 UniProtKB/TrEMBL
NCBI Gene SDC1 ENTREZGENE
PANTHER PTHR10915 UniProtKB/TrEMBL
  PTHR10915:SF5 UniProtKB/TrEMBL
Pfam Syndecan UniProtKB/TrEMBL
PROSITE SYNDECAN UniProtKB/TrEMBL
SMART 4.1m UniProtKB/TrEMBL
UniProt A0A287B0S3_PIG UniProtKB/TrEMBL
  A0A4X1U4Q2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0QSM9_PIG UniProtKB/TrEMBL
  A0A8D0Y314 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1K069 ENTREZGENE, UniProtKB/TrEMBL
  K7GNF5 ENTREZGENE, UniProtKB/TrEMBL
  M5DFN4 ENTREZGENE
VGNC ID VGNC:92654 ENTREZGENE