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 have identical protein binding activity and protein C-terminus binding activity. Involved in several processes, including animal organ development; response to cAMP; and response to hydrogen peroxide. Localizes to 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
Also known as: HSPG; Synd1; syndeca; syndecan; syndecan-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   SD  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2631,562,799 - 31,585,267 (+)NCBI
Rnor_6.0 Ensembl633,885,495 - 33,908,016 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0633,885,576 - 33,908,038 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


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-butoxyethanol  (ISO)
2-methylcholine  (ISO)
3',5'-cyclic AMP  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
adenine  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
bisphenol A  (EXP,ISO)
calcitriol  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
carmustine  (ISO)
chloropicrin  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
cumene  (ISO)
cyclosporin A  (ISO)
daunorubicin  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dioxygen  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fenamidone  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
genistein  (EXP)
graphite  (EXP)
heparin  (ISO)
hydroxychloroquine  (ISO)
ketamine  (EXP)
lipopolysaccharide  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methyltestosterone  (ISO)
miconazole  (EXP)
nimesulide  (EXP)
obeticholic acid  (ISO)
oxaliplatin  (EXP,ISO)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP,ISO)
progesterone  (EXP,ISO)
propiconazole  (ISO)
raloxifene  (ISO)
resiquimod  (ISO)
retinyl acetate  (ISO)
rotenone  (EXP)
simvastatin  (EXP)
sodium arsenate  (ISO)
Soman  (EXP)
sulfasalazine  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
topotecan  (EXP)
triadimefon  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

References

References - curated
1. Bjornson Granqvist A, etal., Am J Physiol Renal Physiol. 2006 Oct;291(4):F722-30. Epub 2006 Apr 18.
2. Brucato S and Villers C, Biochimie. 2002 Jul;84(7):681-6.
3. Brucato S, etal., Eur J Biochem 2002 Jul;269(14):3461-9.
4. Carbone A, etal., Blood. 1998 Oct 1;92(7):2220-8.
5. Carbone A, etal., Blood. 2001 Feb 1;97(3):744-51.
6. Cortes V, etal., Liver Int. 2007 May;27(4):569-81.
7. Endo C, etal., Coron Artery Dis. 1997 Mar-Apr;8(3-4):155-61.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Gharagozlian S, etal., Eur J Nutr. 2006 Oct;45(7):369-75. Epub 2006 Jun 29.
10. GOA data from the GO Consortium
11. Kemp TJ, etal., Biochem Biophys Res Commun. 2003 Jul 25;307(2):416-21.
12. Kim HR, etal., Microb Pathog. 2004 Apr;36(4):219-25.
13. Kojima T, etal., J Biol Chem 1992 Mar 5;267(7):4870-7.
14. Krugel H, etal., J Neurochem. 2006 Apr;97 Suppl 1:74-81.
15. Kwon MJ, etal., J Biol Chem. 2016 Jan 8;291(2):872-81. doi: 10.1074/jbc.M115.685040. Epub 2015 Nov 24.
16. MGD data from the GO Consortium
17. Mulivor AW and Lipowsky HH, Am J Physiol Heart Circ Physiol. 2004 May;286(5):H1672-80. Epub 2004 Jan 2.
18. Nakanishi T, etal., J Biochem. 1997 Feb;121(2):197-205.
19. Olsson U, etal., Diabetes. 2001 Sep;50(9):2126-32.
20. Pipeline to import KEGG annotations from KEGG into RGD
21. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
22. RGD automated data pipeline
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. Sanderson RD and Borset M, Ann Hematol 2002 Mar;81(3):125-35. Epub 2002 Mar 1.
26. Seeley RJ, etal., Annu Rev Nutr 2004;24:133-49.
27. Shworak NW, etal., Haemostasis 1993 Mar;23 Suppl 1:161-76.
28. Steer DL, etal., Dev Biol. 2004 Aug 15;272(2):310-27.
29. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
30. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
31. Worapamorn W, etal., Connect Tissue Res. 2001;42(1):39-48.
32. Worapamorn W, etal., J Periodontal Res. 2002 Aug;37(4):293-9.
33. Wu X, etal., Cancer Res. 2001 Jul 1;61(13):5295-302.
34. Yang Y, etal., J Biol Chem 2003 Apr 11;278(15):12888-93.
35. 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  


Genomics

Comparative Map Data
Sdc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2631,562,799 - 31,585,267 (+)NCBI
Rnor_6.0 Ensembl633,885,495 - 33,908,016 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0633,885,576 - 33,908,038 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl220,200,797 - 20,225,433 (-)EnsemblGRCh38hg38GRCh38
GRCh38220,200,797 - 20,225,475 (-)NCBIGRCh38GRCh38hg38GRCh38
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
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
(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
CanFam3.1 Ensembl1715,222,094 - 15,243,890 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11715,220,906 - 15,243,974 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - 118,011,885 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11487,499,732 - 87,523,122 (+)NCBI
ChlSab1.1 Ensembl1487,499,574 - 87,525,026 (+)Ensembl
Sdc1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247382,920,154 - 2,938,035 (-)NCBI

Position Markers
RH132955  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
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)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295834367603Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
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)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat


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

miRNA Target Status

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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 22 37 35 7 35 51 23 34 11
Low 21 20 6 12 6 8 11 23 12 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000086633   ⟹   ENSRNOP00000072283
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl633,885,495 - 33,908,016 (+)Ensembl
RefSeq Acc Id: NM_013026   ⟹   NP_037158
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
Reference Sequences
RefSeq Acc Id: NP_037158   ⟸   NM_013026
- Peptide Label: precursor
- UniProtKB: P26260 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072283   ⟸   ENSRNOT00000086633

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 33906124 33906125 C A snv F344/NCrl (RGD), SR/JrHsd (RGD), LEW/Crl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3648 AgrOrtholog
Ensembl Genes ENSRNOG00000059947 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000072283 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000086633 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Neurexin-like UniProtKB/Swiss-Prot
  Syndecan UniProtKB/Swiss-Prot
  Syndecan-1 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
SMART 4.1m UniProtKB/Swiss-Prot
TIGR TC216625
UniProt 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 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