Sdc2 (syndecan 2) - Rat Genome Database

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Gene: Sdc2 (syndecan 2) Rattus norvegicus
Analyze
Symbol: Sdc2
Name: syndecan 2
RGD ID: 3649
Description: Enables PDZ domain binding activity and identical protein binding activity. Involved in several processes, including dendrite morphogenesis; positive regulation of epithelial cell migration; and regulation of synapse organization. Located in neuronal cell body. Is active in glutamatergic synapse; postsynaptic membrane; and presynaptic membrane. Human ortholog(s) of this gene implicated in cleft lip and cleft palate. Orthologous to human SDC2 (syndecan 2); PARTICIPATES IN fibroblast growth factor signaling pathway; syndecan signaling pathway; cell-extracellular matrix signaling pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: fibroglycan; heparan sulfate proteoglycan core protein; HSPG; Ryudocan/syndecan 2; SYND2; syndecan-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8766,012,405 - 66,125,101 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl766,108,853 - 66,126,294 (+)EnsemblGRCr8
mRatBN7.2764,127,185 - 64,239,885 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl764,127,110 - 64,241,081 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx766,016,363 - 66,129,168 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0768,218,571 - 68,331,380 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0768,008,023 - 68,120,333 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0771,572,731 - 71,686,139 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl771,572,941 - 71,686,044 (+)Ensemblrn6Rnor6.0
Rnor_5.0771,743,895 - 71,857,365 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4768,290,558 - 68,405,183 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera761,250,356 - 61,362,471 (+)NCBICelera
RGSC_v3.1768,311,497 - 68,426,917 (+)NCBI
Cytogenetic Map7q22NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-schisandrin B  (EXP)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atazanavir sulfate  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium dichloride  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
coumestrol  (ISO)
cyclosporin A  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (EXP,ISO)
diuron  (EXP)
dorsomorphin  (ISO)
edaravone  (EXP)
entinostat  (ISO)
enzyme inhibitor  (ISO)
eugenol  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
furan  (EXP)
gardiquimod  (ISO)
glafenine  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
heparin  (ISO)
Heptachlor epoxide  (ISO)
L-ascorbic acid  (EXP)
L-ethionine  (EXP)
losartan  (EXP)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methapyrilene  (EXP)
methidathion  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
mitoxantrone  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP,ISO)
nickel subsulfide  (EXP)
nickel sulfate  (ISO)
nimesulide  (EXP)
nitric oxide  (ISO)
omeprazole  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
p-toluidine  (EXP)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
perfluorobutyric acid  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
progesterone  (EXP,ISO)
protein kinase inhibitor  (ISO)
quercetin  (ISO)
reactive oxygen species  (EXP)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
senecionine  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
identical protein binding  (IEA,IPI,ISO)
PDZ domain binding  (IEA,IPI,ISO)
protein binding  (IPI,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Syndecan-2 regulates transforming growth factor-beta signaling. Chen L, etal., J Biol Chem. 2004 Apr 16;279(16):15715-8. Epub 2004 Feb 19.
2. Genomic screening identifies novel linkages and provides further evidence for a role of MYH9 in nonsyndromic cleft lip and palate. Chiquet BT, etal., Eur J Hum Genet. 2009 Feb;17(2):195-204. doi: 10.1038/ejhg.2008.149. Epub 2008 Aug 20.
3. Syndecan-2 overexpression regulates adhesion and migration through cooperation with integrin alpha2. Choi S, etal., Biochem Biophys Res Commun. 2009 Jun 26;384(2):231-5. Epub 2009 Apr 24.
4. Cell surface heparan sulfate proteoglycan syndecan-2 induces the maturation of dendritic spines in rat hippocampal neurons. Ethell IM and Yamaguchi Y, J Cell Biol. 1999 Feb 8;144(3):575-86. doi: 10.1083/jcb.144.3.575.
5. EphB/syndecan-2 signaling in dendritic spine morphogenesis. Ethell IM, etal., Neuron. 2001 Sep 27;31(6):1001-13.
6. 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.
7. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
8. Regulated expression and subcellular localization of syndecan heparan sulfate proteoglycans and the syndecan-binding protein CASK/LIN-2 during rat brain development. Hsueh YP and Sheng M, J Neurosci. 1999 Sep 1;19(17):7415-25.
9. Direct interaction of CASK/LIN-2 and syndecan heparan sulfate proteoglycan and their overlapping distribution in neuronal synapses. Hsueh YP, etal., J Cell Biol. 1998 Jul 13;142(1):139-51.
10. Bipartite interaction between neurofibromatosis type I protein (neurofibromin) and syndecan transmembrane heparan sulfate proteoglycans. Hsueh YP, etal., J Neurosci. 2001 Jun 1;21(11):3764-70.
11. Expression of syndecan-2 in the amoeboid microglial cells and its involvement in inflammation in the hypoxic developing brain. Kaur C, etal., Glia. 2009 Feb;57(3):336-49.
12. Lack of modification of 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) rat hepatocarcinogenesis by caffeine, a CYP1A2 inducer, points to complex counteracting influences. Kuribayashi M, etal., Cancer Lett. 2006 Feb 8;232(2):289-99. Epub 2005 Apr 22.
13. 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.
14. Syndecan-2 induces filopodia and dendritic spine formation via the neurofibromin-PKA-Ena/VASP pathway. Lin YL, etal., J Cell Biol. 2007 Jun 4;177(5):829-41. doi: 10.1083/jcb.200608121.
15. The Cardiac Syndecan-2 Interactome. Mathiesen SB, etal., Front Cell Dev Biol. 2020 Aug 28;8:792. doi: 10.3389/fcell.2020.00792. eCollection 2020.
16. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. Molecular cloning of the major cell surface heparan sulfate proteoglycan from rat liver. Pierce A, etal., J Biol Chem 1992 Feb 25;267(6):3894-900.
18. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
19. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
20. GOA pipeline RGD automated data pipeline
21. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
22. 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.
23. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
24. 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.
Additional References at PubMed
PMID:15458844   PMID:18093920   PMID:18256285   PMID:18599487   PMID:19641225   PMID:21555464   PMID:21988832   PMID:23673414   PMID:24498267   PMID:25572401   PMID:25931508   PMID:25979339  
PMID:27068509   PMID:27627962   PMID:28821612  


Genomics

Comparative Map Data
Sdc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8766,012,405 - 66,125,101 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl766,108,853 - 66,126,294 (+)EnsemblGRCr8
mRatBN7.2764,127,185 - 64,239,885 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl764,127,110 - 64,241,081 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx766,016,363 - 66,129,168 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0768,218,571 - 68,331,380 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0768,008,023 - 68,120,333 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0771,572,731 - 71,686,139 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl771,572,941 - 71,686,044 (+)Ensemblrn6Rnor6.0
Rnor_5.0771,743,895 - 71,857,365 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4768,290,558 - 68,405,183 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera761,250,356 - 61,362,471 (+)NCBICelera
RGSC_v3.1768,311,497 - 68,426,917 (+)NCBI
Cytogenetic Map7q22NCBI
SDC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38896,493,813 - 96,611,790 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl896,493,410 - 96,611,790 (+)Ensemblhg38GRCh38
GRCh37897,506,041 - 97,624,018 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36897,575,058 - 97,693,213 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34897,575,057 - 97,693,213NCBI
Celera893,691,860 - 93,810,255 (+)NCBICelera
Cytogenetic Map8q22.1NCBI
HuRef892,711,380 - 92,829,628 (+)NCBIHuRef
CHM1_1897,546,134 - 97,664,535 (+)NCBICHM1_1
T2T-CHM13v2.0897,619,532 - 97,737,516 (+)NCBIT2T-CHM13v2.0
Sdc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391532,920,869 - 33,034,867 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1532,920,869 - 33,035,081 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381532,920,723 - 33,034,721 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1532,920,723 - 33,034,935 (+)Ensemblmm10GRCm38
MGSCv371532,850,478 - 32,964,476 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361532,865,312 - 32,979,310 (+)NCBIMGSCv36mm8
Celera1533,584,115 - 33,695,490 (+)NCBICelera
Cytogenetic Map15B3.1NCBI
cM Map1513.74NCBI
Sdc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541712,462,354 - 12,564,633 (+)Ensembl
ChiLan1.0NW_00495541712,462,354 - 12,563,374 (+)NCBIChiLan1.0ChiLan1.0
SDC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27113,822,721 - 113,937,524 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1889,361,614 - 89,478,168 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0893,118,379 - 93,230,803 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1895,314,910 - 95,428,519 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl895,314,910 - 95,428,519 (+)EnsemblpanPan2panpan1.1
SDC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12940,939,498 - 41,026,694 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2940,939,257 - 41,024,357 (+)EnsemblcanFam3CanFam3.1
ROS_Cfam_1.02941,126,548 - 41,219,188 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.12941,169,044 - 41,261,257 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02941,141,750 - 41,229,172 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02941,600,748 - 41,693,152 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sdc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530338,541,717 - 38,648,722 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647045,967,303 - 46,074,812 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647045,967,816 - 46,074,820 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl440,001,395 - 40,129,697 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1440,003,618 - 40,129,483 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2443,121,719 - 43,248,283 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SDC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1891,451,808 - 91,570,778 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl891,552,647 - 91,568,828 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603949,216,156 - 49,335,471 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247633,809,569 - 3,919,346 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247633,809,850 - 3,920,364 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sdc2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11206,757,323 - 206,872,196 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sdc2
383 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:302
Count of miRNA genes:188
Interacting mature miRNAs:247
Transcripts:ENSRNOT00000007255
Prediction methods: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
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72380760668807606Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74511390390113903Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72663805771638057Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72417947886817926Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74913799967614020Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)75170064396700643Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)731770293110435881Rat
1298525Cm1Cardiac mass QTL 12.7heart mass (VT:0007028)heart wet weight (CMO:0000069)756625161101625161Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73984590284845902Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73299870277998702Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73617876481178764Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)755498584105834451Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)763889858108889858Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74847504993475049Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73617876481178764Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)749682832115766396Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)762963207107963207Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72154197786817926Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)763889858108889858Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)749682832115766396Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)749682832115766396Rat
2303582Gluco53Glucose level QTL 533blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)74860308793603087Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)72718291472182914Rat

Markers in Region
RH129475  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2764,239,449 - 64,239,657 (+)MAPPERmRatBN7.2
Rnor_6.0771,684,605 - 71,684,812NCBIRnor6.0
Rnor_5.0771,855,905 - 71,856,112UniSTSRnor5.0
RGSC_v3.4768,404,748 - 68,404,955UniSTSRGSC3.4
Celera761,362,036 - 61,362,243UniSTS
Cytogenetic Map7q22UniSTS
RH136961  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2764,240,713 - 64,240,889 (+)MAPPERmRatBN7.2
Rnor_6.0771,685,869 - 71,686,044NCBIRnor6.0
Rnor_5.0771,857,169 - 71,857,344UniSTSRnor5.0
RGSC_v3.4768,406,012 - 68,406,187UniSTSRGSC3.4
Celera761,363,300 - 61,363,475UniSTS
Cytogenetic Map7q22UniSTS


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 36 59 6 300 136 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000007255   ⟹   ENSRNOP00000007255
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl764,127,110 - 64,241,081 (+)Ensembl
Rnor_6.0 Ensembl771,572,941 - 71,686,044 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000109204   ⟹   ENSRNOP00000096430
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl764,180,254 - 64,241,081 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000115838   ⟹   ENSRNOP00000097344
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl766,108,853 - 66,126,294 (+)Ensembl
mRatBN7.2 Ensembl764,223,637 - 64,241,081 (+)Ensembl
RefSeq Acc Id: NM_013082   ⟹   NP_037214
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8766,012,405 - 66,125,101 (+)NCBI
mRatBN7.2764,127,185 - 64,239,885 (+)NCBI
Rnor_6.0771,572,731 - 71,685,040 (+)NCBI
Rnor_5.0771,743,895 - 71,857,365 (+)NCBI
RGSC_v3.4768,290,558 - 68,405,183 (+)RGD
Celera761,250,356 - 61,362,471 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_037214 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41355 (Get FASTA)   NCBI Sequence Viewer  
  AAH70890 (Get FASTA)   NCBI Sequence Viewer  
  EDM16437 (Get FASTA)   NCBI Sequence Viewer  
  EDM16438 (Get FASTA)   NCBI Sequence Viewer  
  P34900 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_037214   ⟸   NM_013082
- Peptide Label: precursor
- UniProtKB: P34900 (UniProtKB/Swiss-Prot),   Q6IRK3 (UniProtKB/TrEMBL),   F8WFS4 (UniProtKB/TrEMBL),   A0A9K3Y7Q3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000007255   ⟸   ENSRNOT00000007255
Ensembl Acc Id: ENSRNOP00000097344   ⟸   ENSRNOT00000115838
Ensembl Acc Id: ENSRNOP00000096430   ⟸   ENSRNOT00000109204
Protein Domains
Neurexin/syndecan/glycophorin C

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P34900-F1-model_v2 AlphaFold P34900 1-201 view protein structure

Transcriptome

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

Promoters
RGD ID:13695276
Promoter ID:EPDNEW_R5801
Type:initiation region
Name:Sdc2_1
Description:syndecan 2
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_6.0771,572,957 - 71,573,017EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3649 AgrOrtholog
BioCyc Gene G2FUF-33705 BioCyc
Ensembl Genes ENSRNOG00000004936 Ensembl
IMAGE_CLONE IMAGE:7098631 IMAGE-MGC_LOAD
InterPro Neurexin-like UniProtKB/Swiss-Prot
  Syndecan UniProtKB/Swiss-Prot
  Syndecan/Neurexin_dom UniProtKB/Swiss-Prot
  Syndecan_CS UniProtKB/Swiss-Prot
KEGG Report rno:25615 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91773 IMAGE-MGC_LOAD
NCBI Gene 25615 ENTREZGENE
PANTHER PTHR10915 UniProtKB/Swiss-Prot
  PTHR10915:SF6 UniProtKB/Swiss-Prot
Pfam Syndecan UniProtKB/Swiss-Prot
PhenoGen Sdc2 PhenoGen
PROSITE SYNDECAN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000004936 RatGTEx
SMART 4.1m UniProtKB/Swiss-Prot
TIGR TC228959
UniProt A0A8I6B5M9_RAT UniProtKB/TrEMBL
  A0A9K3Y7Q3 ENTREZGENE, UniProtKB/TrEMBL
  F8WFS4 ENTREZGENE
  P34900 ENTREZGENE
  Q6IRK3 ENTREZGENE
  SDC2_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2001-07-23 Sdc2  syndecan 2      Name updated to reflect Human and Mouse nomenclature 67952 APPROVED
2001-07-23 Sdc2  Ryudocan/syndecan 2      Name withdrawn 67952 WITHDRAWN