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 cellular component biogenesis; positive regulation of protein kinase activity; and ureteric bud development. Located in several cellular components, including costamere; focal adhesion; and membrane raft. 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; 2,3,7,8-tetrachlorodibenzodioxine.
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
Alliance Genes
More Info more info ...
Is Marker For: Strains:   SD  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23153,154,888 - 153,173,576 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3153,154,896 - 153,173,580 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3156,965,401 - 156,984,064 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03165,464,353 - 165,483,016 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03163,208,020 - 163,226,682 (-)NCBIRnor_WKY
Rnor_6.03160,872,503 - 160,891,190 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3160,872,503 - 160,891,190 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03167,052,789 - 167,071,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43155,446,138 - 155,464,825 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13155,352,182 - 155,370,861 (-)NCBI
Celera3151,766,226 - 151,784,912 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,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  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (ISO)
acetazolamide  (ISO)
acetylsalicylic acid  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
Apratastat  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
Benoxacor  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A5  (ISO)
bromobenzene  (EXP)
buspirone  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
caffeine  (ISO)
calcidiol  (EXP)
carbon nanotube  (ISO)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cytarabine  (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)
irinotecan  (ISO)
kojic acid  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
levofloxacin  (EXP)
Licochalcone B  (ISO)
lipopolysaccharide  (ISO)
methylmercury chloride  (ISO)
morphine  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nitroglycerin  (EXP)
omega-6 fatty acid  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
paracetamol  (EXP,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)
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)
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)

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  


Genomics

Comparative Map Data
Sdc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23153,154,888 - 153,173,576 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3153,154,896 - 153,173,580 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3156,965,401 - 156,984,064 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03165,464,353 - 165,483,016 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03163,208,020 - 163,226,682 (-)NCBIRnor_WKY
Rnor_6.03160,872,503 - 160,891,190 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3160,872,503 - 160,891,190 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03167,052,789 - 167,071,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43155,446,138 - 155,464,825 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13155,352,182 - 155,370,861 (-)NCBI
Celera3151,766,226 - 151,784,912 (-)NCBICelera
Cytogenetic Map3q42NCBI
SDC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382045,325,288 - 45,348,424 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2045,325,288 - 45,348,424 (-)EnsemblGRCh38hg38GRCh38
GRCh372043,953,928 - 43,977,064 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362043,387,342 - 43,410,478 (-)NCBINCBI36Build 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 Ensembl
GRCm382164,424,247 - 164,443,188 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2164,424,247 - 164,443,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv372164,249,747 - 164,268,688 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544511,990,916 - 12,009,178 (+)NCBIChiLan1.0ChiLan1.0
SDC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12042,746,597 - 42,769,736 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2042,746,281 - 42,769,737 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02041,656,406 - 41,679,549 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2432,273,638 - 32,293,743 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02433,339,093 - 33,359,207 (-)NCBIROS_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_1.0
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
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247909,146,371 - 9,166,729 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sdc4
43 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
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)343827364169034231Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
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)359242096157323038Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
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)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141339236155617360Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145956084157309487Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3145956084161299569Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat

Markers in Region
D3Wox5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3 RGD
D3Arb12  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
RGSC_v3.13155,353,708 - 155,353,988RGD
Celera3151,767,761 - 151,768,034UniSTS
RH 3.4 Map31426.6UniSTS
RH 3.4 Map31426.6RGD
RH 2.0 Map3980.6RGD
SHRSP x BN Map379.9099RGD
Cytogenetic Map3q42UniSTS
D3Uwm8  
Rat AssemblyChrPosition (strand)SourceJBrowse
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_v3.43155,459,828 - 155,460,014RGDRGSC3.4
RGSC_v3.43155,459,829 - 155,460,014UniSTSRGSC3.4
RGSC_v3.13155,365,864 - 155,366,050RGD
Celera3151,779,918 - 151,780,103UniSTS
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
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 18 53 41 15 41 6 6 33 35 41 11 6
Low 25 4 4 2 5 41 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019386   ⟹   ENSRNOP00000019386
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3153,154,896 - 153,173,580 (-)Ensembl
Rnor_6.0 Ensembl3160,872,503 - 160,891,190 (-)Ensembl
RefSeq Acc Id: NM_012649   ⟹   NP_036781
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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  
  P34901 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036781   ⟸   NM_012649
- Peptide Label: precursor
- UniProtKB: P34901 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019386   ⟸   ENSRNOT00000019386

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 Protein ENSRNOP00000019386 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000019386 ENTREZGENE, 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
Pfam Syndecan UniProtKB/Swiss-Prot
PhenoGen Sdc4 PhenoGen
PROSITE SYNDECAN UniProtKB/Swiss-Prot
SMART 4.1m UniProtKB/Swiss-Prot
TIGR TC204694
UniProt 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