Sdc1 (syndecan 1) - Rat Genome Database

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Gene: Sdc1 (syndecan 1) Rattus norvegicus
Analyze
Symbol: Sdc1
Name: syndecan 1
RGD ID: 3648
Description: Predicted to enable cargo receptor activity and identical protein binding activity. Involved in several processes, including Sertoli cell development; response to cAMP; and response to hydrogen peroxide. Part of protein-containing complex. Used to study familial hyperlipidemia. Biomarker of myocardial infarction; obesity; and proteinuria. Orthologous to human SDC1 (syndecan 1); PARTICIPATES IN altered melanocortin system pathway; melanocortin system pathway; obesity pathway; INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: HSPG; Synd1; syndeca; syndecan; syndecan-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Is Marker For: Strains:   SD
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8637,282,041 - 37,304,503 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl637,297,010 - 37,304,500 (+)EnsemblGRCr8
mRatBN7.2631,562,799 - 31,585,267 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl631,562,739 - 31,585,264 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx631,854,836 - 31,877,298 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0632,170,692 - 32,193,154 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0631,645,292 - 31,667,755 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0633,885,576 - 33,908,038 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl633,885,495 - 33,908,016 (+)Ensemblrn6Rnor6.0
Rnor_5.0643,667,444 - 43,689,903 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4632,253,352 - 32,275,812 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera631,009,934 - 31,032,396 (+)NCBICelera
RGSC_v3.1632,256,304 - 32,278,764 (+)NCBI
Cytogenetic Map6q14NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-colchicine  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,6-dimethoxyphenol  (ISO)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
3',5'-cyclic AMP  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (ISO)
adenine  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
alpha-Zearalanol  (EXP)
amitrole  (EXP)
ammonium chloride  (EXP)
Ampullosporin  (EXP)
Apratastat  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
carmustine  (ISO)
chloropicrin  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
cumene  (ISO)
cyclosporin A  (ISO)
daunorubicin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (EXP,ISO)
diuron  (EXP)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fenamidone  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
furfural  (ISO)
genistein  (EXP)
graphite  (EXP)
heparin  (ISO)
hydroxychloroquine  (ISO)
ivermectin  (ISO)
ketamine  (EXP)
ketoconazole  (EXP,ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (EXP)
methidathion  (ISO)
methimazole  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methyltestosterone  (ISO)
miconazole  (EXP)
nimesulide  (EXP)
obeticholic acid  (ISO)
oxaliplatin  (EXP,ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP,ISO)
progesterone  (EXP,ISO)
propiconazole  (ISO)
raloxifene  (ISO)
resiquimod  (ISO)
resveratrol  (ISO)
retinyl acetate  (ISO)
rotenone  (EXP)
Rutecarpine  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium chloride  (ISO)
Soman  (EXP)
sulfasalazine  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
thiram  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triadimefon  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
WIN 55212-2  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Podocyte proteoglycan synthesis is involved in the development of nephrotic syndrome. Bjornson Granqvist A, etal., Am J Physiol Renal Physiol. 2006 Oct;291(4):F722-30. Epub 2006 Apr 18.
2. Protein kinase C regulation of glypican-1, syndecan-1 and syndecan-4 mRNAs expression during rat Sertoli cell development. Brucato S and Villers C, Biochimie. 2002 Jul;84(7):681-6.
3. Regulation of glypican-1, syndecan-1 and syndecan-4 mRNAs expression by follicle-stimulating hormone, cAMP increase and calcium influx during rat Sertoli cell development. Brucato S, etal., Eur J Biochem 2002 Jul;269(14):3461-9.
4. Expression status of BCL-6 and syndecan-1 identifies distinct histogenetic subtypes of Hodgkin's disease. Carbone A, etal., Blood. 1998 Oct 1;92(7):2220-8.
5. Expression profile of MUM1/IRF4, BCL-6, and CD138/syndecan-1 defines novel histogenetic subsets of human immunodeficiency virus-related lymphomas. Carbone A, etal., Blood. 2001 Feb 1;97(3):744-51.
6. Adenovirus-mediated hepatic syndecan-1 overexpression induces hepatocyte proliferation and hyperlipidaemia in mice. Cortes V, etal., Liver Int. 2007 May;27(4):569-81.
7. Time-dependent increases in syndecan-1 and fibroglycan messenger RNA expression in the infarct zone after experimentally induced myocardial infarction in rats. Endo C, etal., Coron Artery Dis. 1997 Mar-Apr;8(3-4):155-61.
8. 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.
9. Effect of hyperglycemic condition on proteoglycan secretion in cultured human endothelial cells. Gharagozlian S, etal., Eur J Nutr. 2006 Oct;45(7):369-75. Epub 2006 Jun 29.
10. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
11. Changes in gene expression induced by H(2)O(2) in cardiac myocytes. Kemp TJ, etal., Biochem Biophys Res Commun. 2003 Jul 25;307(2):416-21.
12. Role of Syndecan-4 in the cellular invasion of Orientia tsutsugamushi. Kim HR, etal., Microb Pathog. 2004 Apr;36(4):219-25.
13. Molecular cloning and expression of two distinct cDNA-encoding heparan sulfate proteoglycan core proteins from a rat endothelial cell line. Kojima T, etal., J Biol Chem 1992 Mar 5;267(7):4870-7.
14. Transcriptional response to the neuroleptic-like compound Ampullosporin A in the rat ketamine model. Krugel H, etal., J Neurochem. 2006 Apr;97 Suppl 1:74-81.
15. 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.
16. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
17. Inflammation- and ischemia-induced shedding of venular glycocalyx. Mulivor AW and Lipowsky HH, Am J Physiol Heart Circ Physiol. 2004 May;286(5):H1672-80. Epub 2004 Jan 2.
18. 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.
19. Changes in matrix proteoglycans induced by insulin and fatty acids in hepatic cells may contribute to dyslipidemia of insulin resistance. Olsson U, etal., Diabetes. 2001 Sep;50(9):2126-32.
20. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
21. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
22. GOA pipeline RGD automated data pipeline
23. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
25. Syndecan-1 in B lymphoid malignancies. Sanderson RD and Borset M, Ann Hematol 2002 Mar;81(3):125-35. Epub 2002 Mar 1.
26. The critical role of the melanocortin system in the control of energy balance. Seeley RJ, etal., Annu Rev Nutr 2004;24:133-49.
27. Isolation and characterization of ryudocan and syndecan heparan sulfate proteoglycans, core proteins, and cDNAs from a rat endothelial cell line. Shworak NW, etal., Haemostasis 1993 Mar;23 Suppl 1:161-76.
28. Regulation of ureteric bud branching morphogenesis by sulfated proteoglycans in the developing kidney. Steer DL, etal., Dev Biol. 2004 Aug 15;272(2):310-27.
29. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
30. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
31. Differential expression and distribution of syndecan-1 and -2 in the developing periodontium of the rat. Worapamorn W, etal., Connect Tissue Res. 2001;42(1):39-48.
32. Differential expression and distribution of syndecan-1 and -2 in periodontal wound healing of the rat. Worapamorn W, etal., J Periodontal Res. 2002 Aug;37(4):293-9.
33. Suppression subtractive hybridization identified differentially expressed genes in lung adenocarcinoma: ERGIC3 as a novel lung cancer-related gene. Wu M, etal., BMC Cancer. 2013 Feb 1;13:44. doi: 10.1186/1471-2407-13-44.
34. A rare premalignant prostate tumor epithelial cell syndecan-1 forms a fibroblast growth factor-binding complex with progression-promoting ectopic fibroblast growth factor receptor 1. Wu X, etal., Cancer Res. 2001 Jul 1;61(13):5295-302.
35. Heparan sulfate regulates targeting of syndecan-1 to a functional domain on the cell surface. Yang Y, etal., J Biol Chem 2003 Apr 11;278(15):12888-93.
36. [Induction of syndecan-1 expression in parietal cells during gastric mucosal injury by NSAIDs] Yokota K and Satoh T, Nippon Rinsho 2002 Feb;60 Suppl 2:217-21.
Additional References at PubMed
PMID:1639809   PMID:9218485   PMID:9566955   PMID:14681683   PMID:15381701   PMID:15489334   PMID:16982797   PMID:18093920   PMID:18279312   PMID:18762567   PMID:19056867   PMID:20506637  
PMID:22660413   PMID:23525115   PMID:25063885   PMID:25154787   PMID:25972509   PMID:27037369   PMID:27075925   PMID:33378064  


Genomics

Comparative Map Data
Sdc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8637,282,041 - 37,304,503 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl637,297,010 - 37,304,500 (+)EnsemblGRCr8
mRatBN7.2631,562,799 - 31,585,267 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl631,562,739 - 31,585,264 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx631,854,836 - 31,877,298 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0632,170,692 - 32,193,154 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0631,645,292 - 31,667,755 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0633,885,576 - 33,908,038 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl633,885,495 - 33,908,016 (+)Ensemblrn6Rnor6.0
Rnor_5.0643,667,444 - 43,689,903 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4632,253,352 - 32,275,812 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera631,009,934 - 31,032,396 (+)NCBICelera
RGSC_v3.1632,256,304 - 32,278,764 (+)NCBI
Cytogenetic Map6q14NCBI
SDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38220,200,797 - 20,225,475 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl220,200,796 - 20,225,433 (-)Ensemblhg38GRCh38
GRCh37220,400,558 - 20,425,236 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36220,264,039 - 20,288,675 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38128,771,396 - 8,793,716 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl128,771,323 - 8,793,715 (+)Ensemblmm10GRCm38
MGSCv37128,778,202 - 8,800,494 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36128,797,404 - 8,819,696 (+)NCBIMGSCv36mm8
Celera129,156,353 - 9,178,644 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map123.94NCBI
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1715,185,971 - 15,208,368 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01715,373,622 - 15,395,937 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493649311,177,804 - 11,199,678 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3117,987,557 - 118,011,884 (+)EnsemblsusScr11Sscrofa11.1
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1487,499,574 - 87,525,026 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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 1.0HetGla 1.0hetGla2
Sdc1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1729,012,562 - 29,034,836 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sdc1
203 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:500
Count of miRNA genes:259
Interacting mature miRNAs:327
Transcripts:ENSRNOT00000008582
Prediction methods:Microtar, Miranda, 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
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6197587946975879Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)62265388967653889Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6323998948239989Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63118500276185002Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6197587946975879Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6197587946975879Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6144788383Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6197587946975879Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6197587946975879Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6323998948239989Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6323998948239989Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)63332884178328841Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6140163351Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)63093763275937632Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)63332884178328841Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)61608937261967788Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6323998948239989Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)62228825767288257Rat

Markers in Region
RH132955  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2631,584,906 - 31,585,113 (+)MAPPERmRatBN7.2
Rnor_6.0633,907,678 - 33,907,884NCBIRnor6.0
Rnor_5.0643,689,543 - 43,689,749UniSTSRnor5.0
RGSC_v3.4632,275,452 - 32,275,658UniSTSRGSC3.4
Celera631,032,036 - 31,032,242UniSTS
Cytogenetic Map6q14UniSTS


Related Rat Strains
The following Strains have been annotated to Sdc1
SD    


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000086633   ⟹   ENSRNOP00000072283
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl637,298,263 - 37,303,867 (+)Ensembl
mRatBN7.2 Ensembl631,562,739 - 31,585,264 (+)Ensembl
Rnor_6.0 Ensembl633,885,495 - 33,908,016 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000134281   ⟹   ENSRNOP00000104961
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl637,297,010 - 37,304,500 (+)Ensembl
RefSeq Acc Id: NM_013026   ⟹   NP_037158
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8637,282,041 - 37,304,503 (+)NCBI
mRatBN7.2631,562,799 - 31,585,267 (+)NCBI
Rnor_6.0633,885,576 - 33,908,038 (+)NCBI
Rnor_5.0643,667,444 - 43,689,903 (+)NCBI
RGSC_v3.4632,253,352 - 32,275,812 (+)RGD
Celera631,009,934 - 31,032,396 (+)RGD
Sequence:
RefSeq Acc Id: NP_037158   ⟸   NM_013026
- Peptide Label: precursor
- UniProtKB: P26260 (UniProtKB/Swiss-Prot),   A6HAM5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000072283   ⟸   ENSRNOT00000086633
Ensembl Acc Id: ENSRNOP00000104961   ⟸   ENSRNOT00000134281
Protein Domains
Neurexin/syndecan/glycophorin C

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P26260-F1-model_v2 AlphaFold P26260 1-313 view protein structure

Transcriptome

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

Promoters
RGD ID:13694485
Promoter ID:EPDNEW_R5010
Type:initiation region
Name:Sdc1_1
Description:syndecan 1
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_6.0633,885,606 - 33,885,666EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3648 AgrOrtholog
BioCyc Gene G2FUF-38175 BioCyc
Ensembl Genes ENSRNOG00000059947 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000086633.2 UniProtKB/Swiss-Prot
  ENSRNOT00000134281 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:25216 UniProtKB/Swiss-Prot
NCBI Gene 25216 ENTREZGENE
PANTHER PTHR10915 UniProtKB/Swiss-Prot
  PTHR10915:SF5 UniProtKB/Swiss-Prot
Pfam Syndecan UniProtKB/Swiss-Prot
PhenoGen Sdc1 PhenoGen
PROSITE SYNDECAN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000059947 RatGTEx
SMART 4.1m UniProtKB/Swiss-Prot
TIGR TC216625
UniProt A0ABK0LH06_RAT UniProtKB/TrEMBL
  A6HAM4_RAT UniProtKB/TrEMBL
  A6HAM5 ENTREZGENE, UniProtKB/TrEMBL
  A6HAM6_RAT UniProtKB/TrEMBL
  P26260 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Sdc1  syndecan 1      Symbol and Name updated 629477 APPROVED
2003-03-06 Sdc1  syndecan 1  Synd1  Syndecan  Data merged from RGD:3800 628472 PROVISIONAL
2002-06-10 Synd1  Syndecan      Symbol and Name status set to approved 70586 APPROVED
2002-06-10 Sdc1  Syndecan 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_drugs L-type voltage-operated calcium channel blocker, verapamil, stimulated the increase in mRNA expression in sertoli cells of 20 day old animals 625750
gene_expression expressed in Sertoli cells 625750
gene_process regulates Sertoli cell development, involved in signal transduction 625750
gene_regulation mRNA expression was downregulated by intracellular calcium and was modulated by growth factors and cytokine 625750
gene_regulation expression is regulated by PKC activation 625750
gene_regulation expression in is induced by intracellular cAMP at 20 and 30 days of age in Sertoli cells 625750