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Gene: Sdc3 (syndecan 3) Ictidomys tridecemlineatus

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Symbol:

Sdc3

Name:

syndecan 3

RGD ID:

12543996

Description:

ENCODES a protein that exhibits identical protein binding (inferred); INVOLVED IN cell adhesion (ortholog); regulation of cell migration (ortholog); PARTICIPATES IN melanocortin system pathway; syndecan signaling pathway; ASSOCIATED WITH obesity (ortholog); FOUND IN axon (ortholog); plasma membrane (ortholog); protein-containing complex (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

syndecan-3

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):	SDC3 (syndecan 3)	NCBI	Ortholog
Mus musculus (house mouse):	Sdc3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Sdc3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Sdc3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SDC3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SDC3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SDC3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SDC3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Sdc3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Sdc3 (syndecan 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405058	48,375,754 - 48,389,777 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936474	14,204,118 - 14,233,635 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936474	14,203,322 - 14,209,187 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

obesity (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell adhesion (ISO)

cell migration (IEA)

regulation of cell migration (ISO)

Cellular Component

axon (ISO)

cell surface (IEA)

membrane (IEA)

microspike (IEA)

plasma membrane (ISO)

protein-containing complex (ISO)

Molecular Function

identical protein binding (IEA)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

melanocortin system pathway (ISO)

syndecan signaling pathway (ISO)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Sdc3
(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_024405058	48,375,754 - 48,389,777 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936474	14,204,118 - 14,233,635 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936474	14,203,322 - 14,209,187 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SDC3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	30,869,466 - 30,909,735 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	30,869,466 - 30,908,810 (-)	Ensembl			hg38	GRCh38
GRCh37	1	31,342,313 - 31,381,605 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	31,118,567 - 31,154,067 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	1	31,015,074 - 31,050,573	NCBI
Celera	1	29,598,020 - 29,607,292 (-)	NCBI		Celera
Cytogenetic Map	1	p35.2	NCBI
HuRef	1	29,448,414 - 29,487,313 (-)	NCBI		HuRef
CHM1_1	1	31,458,707 - 31,467,979 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	30,721,742 - 30,761,962 (-)	NCBI		T2T-CHM13v2.0

Sdc3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	130,519,855 - 130,553,629 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	130,519,848 - 130,553,630 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	4	130,792,537 - 130,826,318 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	130,792,537 - 130,826,319 (+)	Ensembl			mm10	GRCm38
MGSCv37	4	130,348,452 - 130,382,233 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	4	130,064,654 - 130,098,393 (+)	NCBI		MGSCv36	mm8
Celera	4	128,959,630 - 128,992,669 (+)	NCBI		Celera
Cytogenetic Map	4	D2.2	NCBI
cM Map	4	63.63	NCBI

Sdc3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	148,249,792 - 148,282,524 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	5	148,271,842 - 148,280,614 (+)	Ensembl				GRCr8
mRatBN7.2	5	142,965,659 - 142,998,390 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	142,965,591 - 142,996,480 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	5	145,664,910 - 145,697,641 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	147,434,735 - 147,467,464 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	147,431,294 - 147,464,044 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd	5	147,875,530 - 147,908,277 (+)	NCBI		Dahl_SR_JrHsd
Lyon_Normotensive	5	149,861,964 - 149,894,693 (+)	NCBI		Lyon_Normotensive
Lyon_Hypertensive	5	149,040,442 - 149,073,186 (+)	NCBI		Lyon_Hypertensive
F344_StmMcwi	5	142,620,050 - 142,652,791 (+)	NCBI		F344_StmMcwi
Rnor_6.0	5	148,923,098 - 148,956,404 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	148,923,098 - 148,956,404 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	5	152,628,005 - 152,660,586 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	5	149,486,028 - 149,518,849 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	5	141,427,897 - 141,460,387 (+)	NCBI		Celera
RGSC_v3.1	5	149,497,976 - 149,528,956 (-)	NCBI
Cytogenetic Map	5	q36	NCBI

Sdc3
(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 Ensembl	NW_004955452	9,442,759 - 9,452,027 (-)	Ensembl
ChiLan1.0	NW_004955452	9,442,860 - 9,479,776 (-)	NCBI	ChiLan1.0	ChiLan1.0

SDC3
(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	1	195,930,956 - 195,970,722 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	195,048,132 - 195,087,879 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	30,143,050 - 30,182,795 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	31,169,002 - 31,181,000 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	31,169,002 - 31,178,265 (-)	Ensembl			panPan2	panpan1.1

SDC3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	2	70,081,287 - 70,090,290 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	2	70,056,458 - 70,088,426 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	66,631,617 - 66,667,833 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	2	70,616,352 - 70,652,558 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	2	70,616,352 - 70,652,573 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	2	67,451,512 - 67,487,703 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	2	68,450,471 - 68,486,798 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	2	69,445,397 - 69,485,652 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

SDC3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	87,495,045 - 87,507,235 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	6	87,495,041 - 87,535,689 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	81,263,544 - 81,287,288 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SDC3
(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	20	101,931,276 - 101,970,626 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	101,961,371 - 101,970,950 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666033	14,685,587 - 14,725,086 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Sdc3
(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_female_1.0 Ensembl	NW_004624764	14,316,799 - 14,353,735 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624764	14,316,727 - 14,353,735 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Sdc3
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	1	27,499,382 - 27,532,282 (-)	NCBI		Rrattus_CSIRO_v1

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_005317713	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_078025770	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000117	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JBPVTT010000012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000020902 ⟹ ENSSTOP00000015847

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936474	14,204,118 - 14,233,635 (-)	Ensembl

RefSeq Acc Id:

XM_005317713 ⟹ XP_005317770

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024405058	48,375,754 - 48,389,777 (-)	NCBI
SpeTri2.0	NW_004936474	14,203,322 - 14,209,187 (-)	NCBI

Sequence:

show sequence

GCTCAGCGCTGGCGCAGTGAGAACTTTGAGAGGCCCGTGGACCTGGAGGGCTCTGGGGACGATG
ACTCCTTCCCGGACGATGAACTGGACGACCTCTACTCAGGGTCCGGCTCAGGCTACTTCGAGCA
GGAGTCGGGCCTGGAGACGGCCATGCGGTTCAGCCCCGACGTGGCCCTGGCTGTGTCCACCACG
CCCGCTGTGCTGCCCACCACGGACATCCAGCCTGTGGGCACCCCGTTTGAAGAGCTCCCCTCCG
AGAGCCCCACCCCAGAGCCTGTCACCAGCCCTCCAGTGGTGACAGAGGCCCCAGAGGAGCCTAG
CCAGAGAGCTACCACCATCCCCACCACCACGGCAGCCACCGCTGCCGCCACCACAGGGGCCCCC
ACGGTGGCCACGGTGCCCGCCACTGAGGCCACCGCGGCCCCCAGCATCCCTGCAGCATCCCCGG
CCACGGCCACCACTGCTCTTGTGAGGACCACCGGCATCCGGAGGCTTCCGCCTCTCCCACTGAC
CACAGCCGCCACAGCCCAGGCCACCTCTCCAGCAGCGCCCTCCCCCCCCACCACGGTGGCCGAC
TTAGACACCGAGGCCCCGACACCCAGGCTGGTCACCGCAGCTACCTCCCGGCCAGGAGCCCTTC
CGCGGCCGGCTACCACCCAGGAGCCTGATGTCACTGAGAGGAGCACCCTGCCCCTGGGGACCAC
TGCCCCTGGACCCACAGAGTGGGCTCAGACCCCAACTCCAGAATCCTTCCTGACTACCATCCGG
GATGAACCAGAGGTGCCAGTGAGCAGTGGCCCCAGCGGGGACTTTGAGCTGCCGGAAGAAGAGA
CCACACAGCCAGACACAGCCAATGAGGTGGTGGCTGTGGGAGGGGCGGCGGCCAAGCCGTCACC
TCCACCAGGGACACTGCCCAAGGGTGCCCGCCCAGGCCCCGGCCTCCTGGACAATGCCATCGAC
TCGGGCAGTTCTGCTGCTCAGCTGCCGCAGAAGAGCATCCTGGAGCGGAAGGAGGTGCTCGTAG
CCGTGATTGTGGGCGGGGTCGTGGGTGCCCTCTTCGCTGCCTTCTTGGTCACGCTGCTCATCTA
CCGCATGAAGAAGAAGGATGAAGGCAGCTACACGCTGGAGGAGCCCAAGCAGGCGAGCGTCACC
TACCAGAAGCCTGACAAGCAGGAGGAATTCTATGCCTAGCGGAGCCGCAGTGCCTCCTTGCTGC
CTCGACACCACCCCTCCACCCAGTCCCTGGCCAGCCCCACCAGCCCAGGCCTGGAACTGGGCCC
AGCAGGGAGCCTGGCCCCAGTTCTCCTTTGCCCTCCTTCTCGAGGCCCGCCCAGGCTGCCAGCC
TCACACAGATCATCCCTGAGGAGCAGGGGTGGTTGCTGTCTGCCCCAGACTGTGCCCTTACGAG
CTCATCTCTTGTCCCCCCACCAGCCTGAGGCTTCAGGACCTTATGTCAGATGGACAGGAGGAAG
GAAGCTCCTGATTGGCTGGTGGAATAAGGAGAAGGGGTGGGGCTTGAGATGGGCACCTGGCCCT
GCAGGGCTGGCTGAGGTCTCCTTTTGTGGGCAGAGAGGCCCTCCAGGCTGGCTTTCAGGACCAA
CATGTGGCAGACTCTGCCCTTGAAACAATCTAGACACAGCAACCTCTTGCTCCTGTCCCAGGGC
CTCTCTCTGCCTGGGTGAGAGGGTGCCCTTTGTCACCAGCCTGTTTTGTCCTCGCCTCTCTGGG
GTTGTGGGACCACTCTCCCCTTCCCCTGCCCAGCACCTGTGCCCAAGGCTTCACCTCTTTCTGG
GTCTTCCCCCGAGGAAACAGCTTCCAGAGAGCGCGAGAGCAGCCATTGGTGAGAGGATGCTGCT
GCACACCGCTCCTGGGGGAATACCACAGACATCGTTGCCCACACTCTTCCACACATTGTCATGT
GGCCACAATGACAAGGTCATATACGGTCCTGACCTCCCCACCAATCAAGACATGTTGCAAAAAC
AGA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005317770	(Get FASTA)	NCBI Sequence Viewer
	XP_077881896	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000015847.2
GenBank Protein	KAG3282574	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_005317770 ⟸ XM_005317713

- Sequence:

show sequence

MRFSPDVALAVSTTPAVLPTTDIQPVGTPFEELPSESPTPEPVTSPPVVTEAPEEPSQRATTIP
TTTAATAAATTGAPTVATVPATEATAAPSIPAASPATATTALVRTTGIRRLPPLPLTTAATAQA
TSPAAPSPPTTVADLDTEAPTPRLVTAATSRPGALPRPATTQEPDVTERSTLPLGTTAPGPTEW
AQTPTPESFLTTIRDEPEVPVSSGPSGDFELPEEETTQPDTANEVVAVGGAAAKPSPPPGTLPK
GARPGPGLLDNAIDSGSSAAQLPQKSILERKEVLVAVIVGGVVGALFAAFLVTLLIYRMKKKDE
GSYTLEEPKQASVTYQKPDKQEEFYA

hide sequence

Ensembl Acc Id:

ENSSTOP00000015847 ⟸ ENSSTOT00000020902

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000027125	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000020902.2	UniProtKB/TrEMBL
InterPro	Neurexin-like	UniProtKB/TrEMBL
	Syndecan	UniProtKB/TrEMBL
	Syndecan/Neurexin_dom	UniProtKB/TrEMBL
	Syndecan_CS	UniProtKB/TrEMBL
NCBI Gene	Sdc3	ENTREZGENE
PANTHER	PTHR10915	UniProtKB/TrEMBL
	PTHR10915:SF7	UniProtKB/TrEMBL
Pfam	Syndecan	UniProtKB/TrEMBL
PROSITE	SYNDECAN	UniProtKB/TrEMBL
SMART	4.1m	UniProtKB/TrEMBL
UniProt	I3MUQ2_ICTTR	UniProtKB/TrEMBL

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 - OMIM

RGD Manual Annotations

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - PID (archival)