Sdc3 (syndecan 3) - Rat Genome Database

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Gene: Sdc3 (syndecan 3) Rattus norvegicus
Analyze
Symbol: Sdc3
Name: syndecan 3
RGD ID: 621486
Description: Predicted to enable identical protein binding activity. Involved in cell adhesion and regulation of cell migration. Located in axon and plasma membrane. Part of protein-containing complex. Human ortholog(s) of this gene implicated in obesity. Orthologous to human SDC3 (syndecan 3); PARTICIPATES IN melanocortin system pathway; syndecan signaling pathway; cell-extracellular matrix signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: N-syndecan; neuroglycan; SYND3; syndecan-3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85148,249,792 - 148,282,524 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5148,271,842 - 148,280,614 (+)EnsemblGRCr8
mRatBN7.25142,965,659 - 142,998,390 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5142,965,591 - 142,996,480 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5145,664,910 - 145,697,641 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05147,434,735 - 147,467,464 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05147,431,294 - 147,464,044 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05148,923,098 - 148,956,404 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5148,923,098 - 148,956,404 (+)Ensemblrn6Rnor6.0
Rnor_5.05152,628,005 - 152,660,586 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45149,486,028 - 149,518,849 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5141,427,897 - 141,460,387 (+)NCBICelera
RGSC_v3.15149,497,976 - 149,528,956 (-)NCBI
Cytogenetic Map5q36NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
obesity  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-amino-2-deoxy-D-galactopyranose  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (ISO)
actinomycin D  (EXP,ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (EXP)
amitrole  (EXP)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
Azoxymethane  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
chlordecone  (ISO)
chlorpyrifos  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
decabromodiphenyl ether  (EXP)
dextran sulfate  (ISO)
diquat  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
estriol  (EXP)
ethanol  (ISO)
folic acid  (ISO)
FR900359  (ISO)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP)
hypochlorous acid  (ISO)
lead(0)  (ISO)
methidathion  (ISO)
methimazole  (EXP)
methoxychlor  (EXP)
methylphenidate  (ISO)
Nutlin-3  (ISO)
orphenadrine  (EXP)
paracetamol  (EXP,ISO)
paraquat  (EXP)
pentanal  (ISO)
perfluorooctanoic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
sulfadimethoxine  (EXP)
tamoxifen  (EXP)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
axon  (IDA)
cell surface  (IBA)
membrane  (IDA,IEA)
microspike  (IEA,ISO,ISS)
plasma membrane  (IDA,IEA)
protein-containing complex  (IDA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Pleiotrophin/heparin-binding growth-associated molecule as a mitogen of rat hepatocytes and its role in regeneration and development of liver. Asahina K, etal., Am J Pathol 2002 Jun;160(6):2191-205.
2. A novel role for syndecan-3 in angiogenesis. De Rossi G and Whiteford JR, F1000Res. 2013 Dec 9;2:270. doi: 10.12688/f1000research.2-270.v1. eCollection 2013.
3. Schwann cell adhesion to a novel heparan sulfate binding site in the N-terminal domain of alpha 4 type V collagen is mediated by syndecan-3. Erdman R, etal., J Biol Chem 2002 Mar 1;277(9):7619-25.
4. 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.
5. Bipartite interaction between neurofibromatosis type I protein (neurofibromin) and syndecan transmembrane heparan sulfate proteoglycans. Hsueh YP, etal., J Neurosci. 2001 Jun 1;21(11):3764-70.
6. Osteoblast recruitment and bone formation enhanced by cell matrix-associated heparin-binding growth-associated molecule (HB-GAM). Imai S, etal., J Cell Biol. 1998 Nov 16;143(4):1113-28.
7. Semaphorin 5A is a bifunctional axon guidance cue regulated by heparan and chondroitin sulfate proteoglycans. Kantor DB, etal., Neuron. 2004 Dec 16;44(6):961-75.
8. The Conserved Phenylalanine in the Transmembrane Domain Enhances Heteromeric Interactions of Syndecans. Kwon MJ, etal., J Biol Chem. 2016 Jan 8;291(2):872-81. doi: 10.1074/jbc.M115.685040. Epub 2015 Nov 24.
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. Expression of syndecan-1 and -3 during embryogenesis of the central nervous system in relation to binding with midkine. Nakanishi T, etal., J Biochem. 1997 Feb;121(2):197-205.
11. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
13. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
14. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
15. Isolation of a neuronal cell surface receptor of heparin binding growth-associated molecule (HB-GAM). Identification as N-syndecan (syndecan-3). Raulo E, etal., J Biol Chem. 1994 Apr 29;269(17):12999-3004.
16. GOA pipeline RGD automated data pipeline
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. The critical role of the melanocortin system in the control of energy balance. Seeley RJ, etal., Annu Rev Nutr 2004;24:133-49.
20. Syndecan-3 and perlecan are differentially expressed by progenitors and mature oligodendrocytes and accumulate in the extracellular matrix. Winkler S, etal., J Neurosci Res 2002 Aug 15;69(4):477-87.
Additional References at PubMed
PMID:1556152   PMID:9006931   PMID:12084985   PMID:16384863   PMID:17368428   PMID:18093920   PMID:18599487   PMID:24498267   PMID:25931508   PMID:27068509   PMID:33170350  


Genomics

Comparative Map Data
Sdc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85148,249,792 - 148,282,524 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5148,271,842 - 148,280,614 (+)EnsemblGRCr8
mRatBN7.25142,965,659 - 142,998,390 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5142,965,591 - 142,996,480 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5145,664,910 - 145,697,641 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05147,434,735 - 147,467,464 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05147,431,294 - 147,464,044 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05148,923,098 - 148,956,404 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5148,923,098 - 148,956,404 (+)Ensemblrn6Rnor6.0
Rnor_5.05152,628,005 - 152,660,586 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45149,486,028 - 149,518,849 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5141,427,897 - 141,460,387 (+)NCBICelera
RGSC_v3.15149,497,976 - 149,528,956 (-)NCBI
Cytogenetic Map5q36NCBI
SDC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38130,869,466 - 30,909,735 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl130,869,466 - 30,908,810 (-)Ensemblhg38GRCh38
GRCh37131,342,313 - 31,381,605 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36131,118,567 - 31,154,067 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34131,015,074 - 31,050,573NCBI
Celera129,598,020 - 29,607,292 (-)NCBICelera
Cytogenetic Map1p35.2NCBI
HuRef129,448,414 - 29,487,313 (-)NCBIHuRef
CHM1_1131,458,707 - 31,467,979 (-)NCBICHM1_1
T2T-CHM13v2.0130,721,742 - 30,761,962 (-)NCBIT2T-CHM13v2.0
Sdc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394130,519,855 - 130,553,629 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4130,519,848 - 130,553,630 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm384130,792,537 - 130,826,318 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4130,792,537 - 130,826,319 (+)Ensemblmm10GRCm38
MGSCv374130,348,452 - 130,382,233 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv364130,064,654 - 130,098,393 (+)NCBIMGSCv36mm8
Celera4128,959,630 - 128,992,669 (+)NCBICelera
Cytogenetic Map4D2.2NCBI
cM Map463.63NCBI
Sdc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554529,442,759 - 9,452,027 (-)Ensembl
ChiLan1.0NW_0049554529,442,860 - 9,479,776 (-)NCBIChiLan1.0ChiLan1.0
SDC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21195,930,956 - 195,970,722 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11195,048,132 - 195,087,879 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0130,143,050 - 30,182,795 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1131,169,002 - 31,181,000 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl131,169,002 - 31,178,265 (-)EnsemblpanPan2panpan1.1
SDC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1270,081,287 - 70,090,290 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl270,056,458 - 70,088,426 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha266,631,617 - 66,667,833 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0270,616,352 - 70,652,558 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl270,616,352 - 70,652,573 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1267,451,512 - 67,487,703 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0268,450,471 - 68,486,798 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0269,445,397 - 69,485,652 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sdc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505848,375,754 - 48,389,777 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647414,204,118 - 14,233,635 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647414,203,322 - 14,209,187 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl687,495,045 - 87,507,235 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1687,495,041 - 87,535,689 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2681,263,544 - 81,287,288 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SDC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120101,931,276 - 101,970,626 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20101,961,371 - 101,970,950 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603314,685,587 - 14,725,086 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476414,316,799 - 14,353,735 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462476414,316,727 - 14,353,735 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Sdc3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1127,499,382 - 27,532,282 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sdc3
348 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:588
Count of miRNA genes:237
Interacting mature miRNAs:300
Transcripts:ENSRNOT00000048781
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)5102105698152749382Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)544924861153890773Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116702075161702075Rat
1354583Despr3Despair related QTL34.980.0002locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)5132930505172190305Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5141212838172190305Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)599905133172190305Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134369218156289444Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5133789363172190305Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134369199172190305Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136631198172190305Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112142946157142946Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112142946157142946Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5110770739155770739Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133081618172190305Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)551657967166600247Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138002522170842766Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112142946157142946Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)5141764300172190305Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5148093485172129029Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125969677172190305Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111236572156236572Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5131708216172190305Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114131300159131300Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125969677156302135Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116702075161702075Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112142946157142946Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112142946157142946Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116702075161702075Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)574335621156302135Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116702075161702075Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114131300159131300Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133081618172190305Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)5104262817153890625Rat

Markers in Region
Sdc3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25142,994,052 - 142,994,279 (+)MAPPERmRatBN7.2
Rnor_6.05148,952,067 - 148,952,293NCBIRnor6.0
Rnor_5.05152,656,249 - 152,656,475UniSTSRnor5.0
RGSC_v3.45149,490,139 - 149,490,365UniSTSRGSC3.4
Celera5141,456,050 - 141,456,276UniSTS
Cytogenetic Map5q36UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 355 192 11 142 80 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000048781   ⟹   ENSRNOP00000041634
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5148,271,842 - 148,280,614 (+)Ensembl
mRatBN7.2 Ensembl5142,965,591 - 142,996,480 (+)Ensembl
Rnor_6.0 Ensembl5148,923,098 - 148,956,404 (+)Ensembl
RefSeq Acc Id: NM_053893   ⟹   NP_446345
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85148,249,792 - 148,282,524 (+)NCBI
mRatBN7.25142,965,659 - 142,998,390 (+)NCBI
Rnor_6.05148,923,098 - 148,956,404 (+)NCBI
Rnor_5.05152,628,005 - 152,660,586 (+)NCBI
RGSC_v3.45149,486,028 - 149,518,849 (-)RGD
Celera5141,427,897 - 141,460,387 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446345 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB03284 (Get FASTA)   NCBI Sequence Viewer  
  AAB18192 (Get FASTA)   NCBI Sequence Viewer  
  EDL80599 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000041634
GenBank Protein P33671 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_446345   ⟸   NM_053893
- Peptide Label: precursor
- UniProtKB: P97614 (UniProtKB/Swiss-Prot),   P33671 (UniProtKB/Swiss-Prot),   G3V9B7 (UniProtKB/TrEMBL),   A6ISP8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000041634   ⟸   ENSRNOT00000048781
Protein Domains
Neurexin/syndecan/glycophorin C

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P33671-F1-model_v2 AlphaFold P33671 1-442 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13694086
Promoter ID:EPDNEW_R4610
Type:initiation region
Name:Sdc3_1
Description:syndecan 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05148,923,080 - 148,923,140EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621486 AgrOrtholog
BioCyc Gene G2FUF-39737 BioCyc
Ensembl Genes ENSRNOG00000011927 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000048781 ENTREZGENE
InterPro Neurexin-like UniProtKB/Swiss-Prot
  Syndecan UniProtKB/Swiss-Prot
  Syndecan/Neurexin_dom UniProtKB/Swiss-Prot
  Syndecan_CS UniProtKB/Swiss-Prot
KEGG Report rno:116673 UniProtKB/Swiss-Prot
NCBI Gene 116673 ENTREZGENE
PANTHER PTHR10915 UniProtKB/Swiss-Prot
  PTHR10915:SF7 UniProtKB/Swiss-Prot
Pfam Syndecan UniProtKB/Swiss-Prot
PhenoGen Sdc3 PhenoGen
PROSITE SYNDECAN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000011927 RatGTEx
SMART 4.1m UniProtKB/Swiss-Prot
UniProt A6ISP8 ENTREZGENE, UniProtKB/TrEMBL
  G3V9B7 ENTREZGENE, UniProtKB/TrEMBL
  P33671 ENTREZGENE
  P97614 ENTREZGENE
  SDC3_RAT UniProtKB/Swiss-Prot
UniProt Secondary P97614 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Sdc3  syndecan 3      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Sdc3  syndecan 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function cell adhesion molecule 625469
gene_physical_interaction interacts with a high affinity heparin binding site in the non-collagenous N-terminal domain (NTD) of the alpha4(V) collagen chain and allows Schwann cell adhesion and migration on collagen matrices 625469
gene_process may mediate adhesion-dependent signaling 625469
gene_product transmembrane heparan sulfate proteoglycan 625469