Sdc4 (syndecan 4) - Rat Genome Database

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Gene: Sdc4 (syndecan 4) Rattus norvegicus
Analyze
Symbol: Sdc4
Name: syndecan 4
RGD ID: 3650
Description: Enables fibronectin binding activity; identical protein binding activity; and protein kinase C binding activity. Involved in positive regulation of focal adhesion assembly; positive regulation of stress fiber assembly; and ureteric bud development. Located in cell surface; costamere; and focal adhesion. Used to study bacterial infectious disease. Orthologous to human SDC4 (syndecan 4); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; malaria pathway; INTERACTS WITH 1,3-dinitrobenzene; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: RATRYUDOCA; RYUDOCA; ryudocan core protein; Ryudocan/syndecan 4; SYND4; syndecan-4
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
GRCr83173,574,239 - 173,592,923 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3173,574,239 - 173,593,670 (-)EnsemblGRCr8
mRatBN7.23153,154,888 - 153,173,576 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3153,154,896 - 153,173,580 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3156,965,401 - 156,984,064 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03165,464,353 - 165,483,016 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03163,208,020 - 163,226,682 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03160,872,503 - 160,891,190 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3160,872,503 - 160,891,190 (-)Ensemblrn6Rnor6.0
Rnor_5.03167,052,789 - 167,071,476 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43155,446,138 - 155,464,825 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3151,766,226 - 151,784,912 (-)NCBICelera
RGSC_v3.13155,352,182 - 155,370,861 (-)NCBI
Cytogenetic Map3q42NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acetazolamide  (ISO)
acetylsalicylic acid  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
Apratastat  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
Benoxacor  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (EXP)
beta-lapachone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
bleomycin A5  (ISO)
bromobenzene  (EXP)
buspirone  (EXP)
butanal  (ISO)
Butylbenzyl phthalate  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcidiol  (EXP)
carbon nanotube  (ISO)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
DDE  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dichloroacetic acid  (ISO)
dioxygen  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
fenthion  (ISO)
folic acid  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (EXP)
glafenine  (EXP)
graphite  (EXP)
heparin  (ISO)
hydrogen cyanide  (ISO)
hydrogen peroxide  (ISO)
hydroquinone O-beta-D-glucopyranoside  (ISO)
indometacin  (ISO)
inulin  (ISO)
irinotecan  (ISO)
ketoconazole  (EXP)
kojic acid  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
leflunomide  (ISO)
levofloxacin  (EXP)
Licochalcone B  (ISO)
lipopolysaccharide  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methylmercury chloride  (ISO)
morphine  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nitrates  (ISO)
nitroglycerin  (EXP)
Nutlin-3  (ISO)
omega-6 fatty acid  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
permethrin  (ISO)
phenethyl caffeate  (EXP)
phenformin  (EXP)
phenobarbital  (EXP,ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP,ISO)
potassium cyanide  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
senecionine  (ISO)
sevoflurane  (EXP)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
succimer  (ISO)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
temozolomide  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP,ISO)
Triptolide  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cell surface  (IBA,IDA,IEA,ISO)
costamere  (IDA)
extracellular region  (IEA)
focal adhesion  (IDA)
membrane  (IEA)
plasma membrane  (TAS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Regulation of inositol phospholipid binding and signaling through syndecan-4. Couchman JR, etal., J Biol Chem 2002 Dec 20;277(51):49296-303.
3. Gene expression profile in diabetic KK/Ta mice. Fan Q, etal., Kidney Int. 2003 Dec;64(6):1978-85.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. Syndecan-4 associates with alpha-actinin. Greene DK, etal., J Biol Chem 2003 Feb 28;278(9):7617-23. Epub 2002 Dec 18.
7. miR-18a-5p MicroRNA Increases Vascular Smooth Muscle Cell Differentiation by Downregulating Syndecan4. Kee HJ, etal., Korean Circ J. 2014 Jul;44(4):255-63. doi: 10.4070/kcj.2014.44.4.255. Epub 2014 Jul 25.
8. Role of Syndecan-4 in the cellular invasion of Orientia tsutsugamushi. Kim HR, etal., Microb Pathog. 2004 Apr;36(4):219-25.
9. 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.
10. Plasma levels of syndecan-4 (ryudocan) are elevated in patients with acute myocardial infarction. Kojima T, etal., Thromb Haemost. 2001 May;85(5):793-9.
11. 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.
12. Direct binding of syndecan-4 cytoplasmic domain to the catalytic domain of protein kinase C alpha (PKC alpha) increases focal adhesion localization of PKC alpha. Lim ST, etal., J Biol Chem. 2003 Apr 18;278(16):13795-802. Epub 2003 Feb 5.
13. Control of morphology, cytoskeleton and migration by syndecan-4. Longley RL, etal., J Cell Sci. 1999 Oct;112 ( Pt 20):3421-31.
14. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
15. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
17. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
18. GOA pipeline RGD automated data pipeline
19. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
20. 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.
21. 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.
22. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
23. Clustering induces redistribution of syndecan-4 core protein into raft membrane domains. Tkachenko E and Simons M, J Biol Chem. 2002 May 31;277(22):19946-51. Epub 2002 Mar 11.
24. Localization of the transmembrane proteoglycan syndecan-4 and its regulatory kinases in costameres of rat cardiomyocytes: a deconvolution microscopic study. VanWinkle WB, etal., Anat Rec 2002 Sep 1;268(1):38-46.
25. Syndecan-4 binding to the high affinity heparin-binding domain of fibronectin drives focal adhesion formation in fibroblasts. Woods A, etal., Arch Biochem Biophys. 2000 Feb 1;374(1):66-72.
Additional References at PubMed
PMID:11456484   PMID:12509413   PMID:15226395   PMID:15381701   PMID:16310216   PMID:16787950   PMID:16924669   PMID:17728463   PMID:17879962   PMID:18093920   PMID:19199708   PMID:19350579  
PMID:19581409   PMID:19723805   PMID:20501378   PMID:21518435   PMID:21949132   PMID:22307630   PMID:22504297   PMID:22645300   PMID:22660413   PMID:22871113   PMID:23376485   PMID:23760952  
PMID:24558194   PMID:25074804   PMID:25174688   PMID:25491150   PMID:25931508   PMID:25979339   PMID:26193076   PMID:26272378   PMID:27830760   PMID:32811537   PMID:38891079  


Genomics

Comparative Map Data
Sdc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83173,574,239 - 173,592,923 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3173,574,239 - 173,593,670 (-)EnsemblGRCr8
mRatBN7.23153,154,888 - 153,173,576 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3153,154,896 - 153,173,580 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3156,965,401 - 156,984,064 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03165,464,353 - 165,483,016 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03163,208,020 - 163,226,682 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03160,872,503 - 160,891,190 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3160,872,503 - 160,891,190 (-)Ensemblrn6Rnor6.0
Rnor_5.03167,052,789 - 167,071,476 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43155,446,138 - 155,464,825 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3151,766,226 - 151,784,912 (-)NCBICelera
RGSC_v3.13155,352,182 - 155,370,861 (-)NCBI
Cytogenetic Map3q42NCBI
SDC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382045,325,288 - 45,348,424 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2045,325,288 - 45,348,425 (-)Ensemblhg38GRCh38
GRCh372043,953,928 - 43,977,064 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362043,387,342 - 43,410,478 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342043,387,343 - 43,410,478NCBI
Celera2040,662,456 - 40,685,588 (-)NCBICelera
Cytogenetic Map20q13.12NCBI
HuRef2040,695,444 - 40,718,573 (-)NCBIHuRef
CHM1_12043,856,488 - 43,879,617 (-)NCBICHM1_1
T2T-CHM13v2.02047,061,165 - 47,084,301 (-)NCBIT2T-CHM13v2.0
Sdc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392164,266,167 - 164,285,512 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2164,266,167 - 164,285,807 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm382164,424,247 - 164,443,188 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2164,424,247 - 164,443,887 (-)Ensemblmm10GRCm38
MGSCv372164,249,747 - 164,268,688 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362164,115,452 - 164,134,393 (-)NCBIMGSCv36mm8
Celera2170,361,365 - 170,380,306 (-)NCBICelera
Cytogenetic Map2H3NCBI
cM Map285.16NCBI
Sdc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544511,990,792 - 12,011,553 (+)Ensembl
ChiLan1.0NW_00495544511,990,916 - 12,009,178 (+)NCBIChiLan1.0ChiLan1.0
SDC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22151,058,899 - 51,082,046 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12051,052,007 - 51,075,147 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02041,656,406 - 41,679,549 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12042,746,597 - 42,769,736 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2042,746,281 - 42,769,737 (-)EnsemblpanPan2panpan1.1
SDC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12432,628,704 - 32,648,809 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2432,630,437 - 32,649,114 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2432,273,638 - 32,293,743 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02433,339,093 - 33,359,207 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2433,339,093 - 33,359,179 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12432,600,350 - 32,620,457 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02432,715,919 - 32,736,026 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02433,259,679 - 33,280,258 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sdc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640192,074,895 - 192,108,750 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365147,555,685 - 7,562,391 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365147,528,538 - 7,562,391 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11747,650,387 - 47,670,499 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21753,254,792 - 53,270,726 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SDC4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1218,490,474 - 18,513,329 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl218,490,485 - 18,513,332 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605067,132,278 - 67,155,156 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdc4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247909,145,745 - 9,169,526 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247909,146,371 - 9,166,729 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sdc4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v15153,522,211 - 153,539,195 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:226
Count of miRNA genes:155
Interacting mature miRNAs:188
Transcripts:ENSRNOT00000019386
Prediction methods: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
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3141555229186555229Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141555229186555229Rat
1582233Insul10Insulin level QTL 105.40.0015blood insulin amount (VT:0001560)serum insulin level times blood glucose level (CMO:0002040)3133259579178259579Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3166376089177728348Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3141555229186555229Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3141555229186555229Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3129154923182114333Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3141555229186555229Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3141555229186555229Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161492708189428310Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3166376089189428310Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161799493176036425Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3133134628178134628Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3161799270187311134Rat
1582213Insul6Insulin level QTL 63.70.0009blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3166376089189428310Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3142898802187898802Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)3145335553189428310Rat
1582256Insul9Insulin level QTL 94.40.0016blood insulin amount (VT:0001560)absolute change in serum insulin level (CMO:0002038)3155759447189428310Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3139299381184299381Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3141508991177728348Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)3131036586176036586Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3137114333182114333Rat
1582248Insul7Insulin level QTL 73.90.0041blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)3131036586176036586Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3141555229186555229Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat

Markers in Region
D3Wox5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3 RGD
D3Arb12  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr83173,575,773 - 173,576,051 (+)Marker Load Pipeline
mRatBN7.23153,156,423 - 153,156,701 (+)MAPPERmRatBN7.2
Rnor_6.03160,874,038 - 160,874,317NCBIRnor6.0
Rnor_5.03167,054,324 - 167,054,603UniSTSRnor5.0
RGSC_v3.43155,447,672 - 155,447,952RGDRGSC3.4
RGSC_v3.43155,447,673 - 155,447,952UniSTSRGSC3.4
Celera3151,767,761 - 151,768,034UniSTS
RGSC_v3.13155,353,708 - 155,353,988RGD
RH 3.4 Map31426.6RGD
RH 3.4 Map31426.6UniSTS
RH 2.0 Map3980.6RGD
SHRSP x BN Map379.9099RGD
Cytogenetic Map3q42UniSTS
D3Uwm8  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr83173,587,927 - 173,588,113 (+)Marker Load Pipeline
mRatBN7.23153,168,578 - 153,168,764 (+)MAPPERmRatBN7.2
Rnor_6.03160,886,194 - 160,886,379NCBIRnor6.0
Rnor_5.03167,066,480 - 167,066,665UniSTSRnor5.0
RGSC_v3.43155,459,829 - 155,460,014UniSTSRGSC3.4
RGSC_v3.43155,459,828 - 155,460,014RGDRGSC3.4
Celera3151,779,918 - 151,780,103UniSTS
RGSC_v3.13155,365,864 - 155,366,050RGD
Cytogenetic Map3q42UniSTS
RH127752  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23153,155,050 - 153,155,248 (+)MAPPERmRatBN7.2
Rnor_6.03160,872,666 - 160,872,863NCBIRnor6.0
Rnor_5.03167,052,952 - 167,053,149UniSTSRnor5.0
RGSC_v3.43155,446,301 - 155,446,498UniSTSRGSC3.4
Celera3151,766,389 - 151,766,586UniSTS
RH 3.4 Map31423.1UniSTS
Cytogenetic Map3q42UniSTS


Related Rat Strains
The following Strains have been annotated to Sdc4
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 67 164 91 90 59 91 59 6 355 191 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000019386   ⟹   ENSRNOP00000019386
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3173,574,239 - 173,592,923 (-)Ensembl
mRatBN7.2 Ensembl3153,154,896 - 153,173,580 (-)Ensembl
Rnor_6.0 Ensembl3160,872,503 - 160,891,190 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000156795   ⟹   ENSRNOP00000100184
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3173,574,239 - 173,593,670 (-)Ensembl
RefSeq Acc Id: NM_012649   ⟹   NP_036781
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83173,574,239 - 173,592,923 (-)NCBI
mRatBN7.23153,154,888 - 153,173,576 (-)NCBI
Rnor_6.03160,872,503 - 160,891,190 (-)NCBI
Rnor_5.03167,052,789 - 167,071,476 (-)NCBI
RGSC_v3.43155,446,138 - 155,464,825 (-)RGD
Celera3151,766,226 - 151,784,912 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036781 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA73167 (Get FASTA)   NCBI Sequence Viewer  
  AAB26725 (Get FASTA)   NCBI Sequence Viewer  
  EDL96527 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019386
  ENSRNOP00000019386.2
GenBank Protein P34901 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_036781   ⟸   NM_012649
- Peptide Label: precursor
- UniProtKB: P34901 (UniProtKB/Swiss-Prot),   A6JX82 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000019386   ⟸   ENSRNOT00000019386
Ensembl Acc Id: ENSRNOP00000100184   ⟸   ENSRNOT00000156795
Protein Domains
Neurexin/syndecan/glycophorin C

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P34901-F1-model_v2 AlphaFold P34901 1-202 view protein structure

Transcriptome

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

Promoters
RGD ID:13692656
Promoter ID:EPDNEW_R3179
Type:single initiation site
Name:Sdc4_1
Description:syndecan 4
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_6.03160,891,197 - 160,891,257EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3650 AgrOrtholog
BioCyc Gene G2FUF-46859 BioCyc
Ensembl Genes ENSRNOG00000014297 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000019386 ENTREZGENE
  ENSRNOT00000019386.4 UniProtKB/Swiss-Prot
InterPro Neurexin-like UniProtKB/Swiss-Prot
  Syndecan UniProtKB/Swiss-Prot
  Syndecan/Neurexin_dom UniProtKB/Swiss-Prot
  Syndecan_CS UniProtKB/Swiss-Prot
KEGG Report rno:24771 UniProtKB/Swiss-Prot
NCBI Gene 24771 ENTREZGENE
PANTHER PTHR10915 UniProtKB/Swiss-Prot
  SYNDECAN-4 UniProtKB/Swiss-Prot
Pfam Syndecan UniProtKB/Swiss-Prot
PhenoGen Sdc4 PhenoGen
PROSITE SYNDECAN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000014297 RatGTEx
SMART 4.1m UniProtKB/Swiss-Prot
TIGR TC204694
UniProt A0ABK0KYP7_RAT UniProtKB/TrEMBL
  A6JX82 ENTREZGENE, UniProtKB/TrEMBL
  P34901 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2001-07-23 Sdc4  syndecan 4      Name updated to reflect Human and Mouse nomenclature 67952 APPROVED
2001-07-23 Sdc4  Ryudocan/syndecan 4      Name withdrawn 67952 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in sertoli cells 625750
gene_expression mRNA is expressed in Sertoli cells 625750
gene_process regulates sertoli cell development 625750
gene_regulation high levels of intracellular cAMP level increased RNA expression in 30 day old animals 625750
gene_regulation expression is induced by intracellular cAMP in Sertoli cells at 30 days of age but not at earlier stages 625750
gene_regulation FSH, the main regulator of sertoli cell function did not effect the mRNA expression 625750
gene_regulation expression is regulated by PKC activation 625750