Sdc1 (syndecan 1) - Rat Genome Database

Name: Sdc1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Sdc1 (syndecan 1) Heterocephalus glaber

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Symbol:

Sdc1

Name:

syndecan 1

RGD ID:

18927430

Description:

ENCODES a protein that exhibits cargo receptor activity (ortholog); identical protein binding (ortholog); INVOLVED IN canonical Wnt signaling pathway (ortholog); myoblast development (ortholog); positive regulation of exosomal secretion (ortholog); PARTICIPATES IN altered melanocortin system pathway; melanocortin system pathway; obesity pathway; ASSOCIATED WITH COVID-19 (ortholog); familial hyperlipidemia (ortholog); Hodgkin's lymphoma (ortholog); FOUND IN cell surface (ortholog); external side of plasma membrane (ortholog); plasma membrane (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

syndecan-1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	SDC1 (syndecan 1)	NCBI	Ortholog
Mus musculus (house mouse):	Sdc1 (syndecan 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Sdc1 (syndecan 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Sdc1 (syndecan 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SDC1 (syndecan 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SDC1 (syndecan 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Sdc1 (syndecan 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SDC1 (syndecan 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SDC1 (syndecan 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly

Position:

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624738	2,920,154 - 2,938,035 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

COVID-19 (ISO)

familial hyperlipidemia (ISO)

Hodgkin's lymphoma (ISO)

hyperglycemia (ISO)

Inflammation (ISO)

long QT syndrome (ISO)

lung adenocarcinoma (ISO)

Lymphoma, AIDS-Related (ISO)

malignant mesothelioma (ISO)

myocardial infarction (ISO)

obesity (ISO)

proteinuria (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

canonical Wnt signaling pathway (ISO)

myoblast development (ISO)

positive regulation of exosomal secretion (ISO)

positive regulation of extracellular exosome assembly (ISO)

receptor-mediated endocytosis (ISO)

response to calcium ion (ISO)

response to cAMP (ISO)

response to glucocorticoid (ISO)

response to hydrogen peroxide (ISO)

response to toxic substance (ISO)

Sertoli cell development (ISO)

striated muscle cell development (ISO)

ureteric bud development (ISO)

Cellular Component

cell surface (ISO)

external side of plasma membrane (ISO)

plasma membrane (ISO)

protein-containing complex (ISO)

Molecular Function

cargo receptor activity (ISO)

identical protein binding (ISO)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

altered melanocortin system pathway (ISO)

melanocortin system pathway (ISO)

obesity pathway (ISO)

syndecan signaling pathway (ISO)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Sdc1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624738	2,920,154 - 2,938,035 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

SDC1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	20,200,797 - 20,225,475 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	20,200,797 - 20,225,433 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	20,400,558 - 20,425,236 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	20,264,039 - 20,288,675 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	20,322,187 - 20,346,555	NCBI
Celera	2	20,262,845 - 20,287,481 (-)	NCBI		Celera
Cytogenetic Map	2	p24.1	NCBI
HuRef	2	20,158,155 - 20,182,491 (-)	NCBI		HuRef
CHM1_1	2	20,329,922 - 20,354,554 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	2	20,234,345 - 20,259,019 (-)	NCBI		T2T-CHM13v2.0

Sdc1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	8,821,396 - 8,843,716 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	8,821,323 - 8,843,715 (+)	Ensembl		GRCm39 Ensembl
GRCm38	12	8,771,396 - 8,793,716 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	8,771,323 - 8,793,715 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	8,778,202 - 8,800,494 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	8,797,404 - 8,819,696 (+)	NCBI		MGSCv36	mm8
Celera	12	9,156,353 - 9,178,644 (+)	NCBI		Celera
Cytogenetic Map	12	A1.1	NCBI
cM Map	12	3.94	NCBI

Sdc1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	37,282,041 - 37,304,503 (+)	NCBI		GRCr8
mRatBN7.2	6	31,562,799 - 31,585,267 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	31,562,739 - 31,585,264 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	31,854,836 - 31,877,298 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	32,170,692 - 32,193,154 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	31,645,292 - 31,667,755 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	33,885,576 - 33,908,038 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	33,885,495 - 33,908,016 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	43,667,444 - 43,689,903 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	32,253,352 - 32,275,812 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	32,256,304 - 32,278,764 (+)	NCBI
Celera	6	31,009,934 - 31,032,396 (+)	NCBI		Celera
Cytogenetic Map	6	q14	NCBI

Sdc1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955469	2,762,696 - 2,773,697 (-)	NCBI	ChiLan1.0	ChiLan1.0

SDC1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	12	106,303,344 - 106,327,699 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	106,307,316 - 106,331,671 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	20,187,249 - 20,211,567 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	20,302,589 - 20,309,848 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	20,302,589 - 20,309,848 (-)	Ensembl	panpan1.1		panPan2

SDC1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	17	15,220,906 - 15,243,974 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	17	15,222,094 - 15,243,890 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	17	15,185,971 - 15,208,368 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	17	15,373,622 - 15,395,937 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	17	15,373,628 - 15,395,946 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	17	15,227,151 - 15,249,524 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	17	15,233,919 - 15,256,296 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	17	15,265,578 - 15,287,885 (-)	NCBI		UU_Cfam_GSD_1.0

Sdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024406292	59,639,887 - 59,661,785 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936493	11,177,708 - 11,199,804 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936493	11,177,804 - 11,199,678 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SDC1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	117,987,557 - 118,011,884 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	117,987,585 - 118,011,886 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	125,988,758 - 126,027,188 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SDC1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	14	87,499,732 - 87,523,122 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	87,499,574 - 87,525,026 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	24,701,281 - 24,725,764 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_004839043	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AHKG01015481	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_004839043 ⟹ XP_004839100

Type:

CODING

Position:

Naked Mole-Rat Assembly	Chr	Position (strand)	Source
HetGla 1.0	NW_004624738	2,920,154 - 2,938,035 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_004839100	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_004839100 ⟸ XM_004839043

Additional Information

External Database Links

Database	Acc Id	Source(s)
NCBI Gene	Sdc1	ENTREZGENE

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - PID (archival)