Sdc1 (syndecan 1) - Rat Genome Database

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Gene: Sdc1 (syndecan 1) Ictidomys tridecemlineatus
Analyze
Symbol: Sdc1
Name: syndecan 1
RGD ID: 12736864
Description: ENCODES a protein that exhibits identical protein binding (inferred); protein C-terminus binding (inferred); INVOLVED IN canonical Wnt signaling pathway (ortholog); inflammatory response (ortholog); odontogenesis (ortholog); PARTICIPATES IN altered melanocortin system pathway; melanocortin system pathway; obesity pathway; ASSOCIATED WITH COVID-19 (ortholog); cranioectodermal dysplasia 2 (ortholog); familial hyperlipidemia (ortholog); FOUND IN protein-containing complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: syndecan-1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629259,639,887 - 59,661,785 (-)NCBI
SpeTri2.0NW_00493649311,177,804 - 11,199,678 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Genomics

Comparative Map Data
Sdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629259,639,887 - 59,661,785 (-)NCBI
SpeTri2.0NW_00493649311,177,804 - 11,199,678 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38220,200,797 - 20,225,475 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl220,200,797 - 20,225,433 (-)EnsemblGRCh38hg38GRCh38
GRCh37220,400,558 - 20,425,236 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36220,264,039 - 20,288,675 (-)NCBINCBI36hg18NCBI36
Build 34220,322,187 - 20,346,555NCBI
Celera220,262,845 - 20,287,481 (-)NCBI
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 (-)NCBI
Sdc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39128,821,396 - 8,843,716 (+)NCBIGRCm39mm39
GRCm39 Ensembl128,821,323 - 8,843,715 (+)Ensembl
GRCm38128,771,396 - 8,793,716 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl128,771,323 - 8,793,715 (+)EnsemblGRCm38mm10GRCm38
MGSCv37128,778,202 - 8,800,494 (+)NCBIGRCm37mm9NCBIm37
MGSCv36128,797,404 - 8,819,696 (+)NCBImm8
Celera129,156,353 - 9,178,644 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map123.94NCBI
Sdc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2631,562,799 - 31,585,267 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl631,562,739 - 31,585,264 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
PanPan1.12A20,302,589 - 20,309,848 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A20,302,589 - 20,309,848 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A20,187,249 - 20,211,567 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.01715,373,622 - 15,395,937 (-)NCBI
ROS_Cfam_1.0 Ensembl1715,373,628 - 15,395,946 (-)Ensembl
UMICH_Zoey_3.11715,227,151 - 15,249,524 (-)NCBI
UNSW_CanFamBas_1.01715,233,919 - 15,256,296 (-)NCBI
UU_Cfam_GSD_1.01715,265,578 - 15,287,885 (-)NCBI
SDC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3117,987,557 - 118,011,885 (+)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
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11487,499,732 - 87,523,122 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1487,499,574 - 87,525,026 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604524,701,281 - 24,725,764 (-)NCBIVero_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_1.0hetGla2


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005322611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAESOR010001352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: XM_005322611   ⟹   XP_005322668
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440629259,639,887 - 59,661,785 (-)NCBI
SpeTri2.0NW_00493649311,177,804 - 11,199,678 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005322668 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein KAG3267637 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_005322668   ⟸   XM_005322611
- UniProtKB: I3NFD8 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
4.1m


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000028519 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSSTOP00000023085 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000019416 UniProtKB/TrEMBL
InterPro Neurexin-like UniProtKB/TrEMBL
  Syndecan UniProtKB/TrEMBL
  Syndecan-1 UniProtKB/TrEMBL
  Syndecan/Neurexin_dom UniProtKB/TrEMBL
  Syndecan_CS 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 I3NFD8 ENTREZGENE, UniProtKB/TrEMBL