SDC1 (syndecan 1) - Rat Genome Database

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Gene: SDC1 (syndecan 1) Homo sapiens
Analyze
Symbol: SDC1
Name: syndecan 1
RGD ID: 730864
HGNC Page HGNC
Description: Enables identical protein binding activity and protein C-terminus binding activity. Involved in positive regulation of exosomal secretion; positive regulation of extracellular exosome assembly; and striated muscle cell development. Located in cell surface. Biomarker of Hodgkin's lymphoma and hyperglycemia.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: CD138; CD138 antigen; heparan sulfate proteoglycan fibroblast growth factor receptor; SDC; SYND1; syndecan; syndecan proteoglycan 1; syndecan-1
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38220,200,797 - 20,225,475 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl220,200,797 - 20,225,433 (-)EnsemblGRCh38hg38GRCh38
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
T2T-CHM13v2.0220,234,345 - 20,259,019 (-)NCBI
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  (EXP)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
2-methylcholine  (EXP)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3H-1,2-dithiole-3-thione  (ISO)
6-propyl-2-thiouracil  (ISO)
acrolein  (EXP)
acrylamide  (EXP)
adenine  (EXP)
afimoxifene  (EXP)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP,ISO)
alpha-pinene  (EXP)
ammonium chloride  (ISO)
Apratastat  (EXP)
arsane  (EXP)
arsenic atom  (EXP)
arsenous acid  (EXP)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
calcitriol  (EXP)
camptothecin  (EXP)
carbon nanotube  (ISO)
carbonyl sulfide  (ISO)
carmustine  (EXP)
chloropicrin  (EXP)
cisplatin  (EXP,ISO)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (EXP)
corticosterone  (ISO)
cumene  (ISO)
cyclosporin A  (EXP)
daunorubicin  (EXP)
deoxynivalenol  (EXP)
dexamethasone  (EXP)
diarsenic trioxide  (EXP)
dioxygen  (EXP,ISO)
diuron  (ISO)
doxorubicin  (EXP,ISO)
enzyme inhibitor  (EXP)
ethyl methanesulfonate  (EXP)
etoposide  (EXP)
fenamidone  (ISO)
flavonoids  (ISO)
folic acid  (ISO)
formaldehyde  (EXP)
genistein  (ISO)
graphite  (ISO)
heparin  (EXP)
hydroxychloroquine  (EXP)
ivermectin  (EXP)
ketamine  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (ISO)
methotrexate  (EXP)
methyl methanesulfonate  (EXP)
methyltestosterone  (EXP)
miconazole  (ISO)
nimesulide  (ISO)
obeticholic acid  (EXP)
oxaliplatin  (EXP,ISO)
ozone  (EXP)
paracetamol  (EXP)
paraquat  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
pirinixic acid  (ISO)
progesterone  (EXP,ISO)
propiconazole  (ISO)
raloxifene  (EXP)
resiquimod  (ISO)
resveratrol  (EXP)
retinyl acetate  (ISO)
rotenone  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP)
Soman  (ISO)
sulfasalazine  (EXP)
sunitinib  (EXP)
temozolomide  (EXP)
tetrachloromethane  (ISO)
thimerosal  (EXP)
topotecan  (ISO)
triadimefon  (ISO)
valproic acid  (EXP)
vancomycin  (ISO)
vinclozolin  (ISO)
WIN 55212-2  (EXP)
zoledronic acid  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Additional References at PubMed
PMID:1339431   PMID:1442271   PMID:1644217   PMID:1664683   PMID:2173154   PMID:2324102   PMID:2519615   PMID:7592855   PMID:7592967   PMID:7690138   PMID:7959737   PMID:8118875  
PMID:8125298   PMID:8163535   PMID:8570206   PMID:8889548   PMID:9050911   PMID:9089390   PMID:9111037   PMID:9294130   PMID:9342064   PMID:9548182   PMID:9565572   PMID:9566955  
PMID:9660868   PMID:9792716   PMID:9857223   PMID:10497173   PMID:10506830   PMID:11024024   PMID:11168765   PMID:11179419   PMID:11567105   PMID:11830493   PMID:11877089   PMID:12091355  
PMID:12144130   PMID:12464176   PMID:12477932   PMID:12660231   PMID:12749851   PMID:12824007   PMID:12879463   PMID:12885232   PMID:12902511   PMID:12904296   PMID:12920224   PMID:12947106  
PMID:12975379   PMID:14521955   PMID:14630925   PMID:14637022   PMID:14645569   PMID:14701864   PMID:14744776   PMID:14972511   PMID:15126321   PMID:15292202   PMID:15297422   PMID:15383330  
PMID:15459490   PMID:15479743   PMID:15489334   PMID:15648090   PMID:15728209   PMID:15743035   PMID:15770719   PMID:15797855   PMID:15886501   PMID:15902740   PMID:16007225   PMID:16020957  
PMID:16132527   PMID:16157597   PMID:16247452   PMID:16286510   PMID:16341674   PMID:16636895   PMID:16720645   PMID:16773719   PMID:16778379   PMID:16817962   PMID:16840194   PMID:16857657  
PMID:16884912   PMID:16934308   PMID:16945147   PMID:16982797   PMID:17149710   PMID:17314405   PMID:17339423   PMID:17413980   PMID:17431390   PMID:17455248   PMID:17579341   PMID:17625591  
PMID:18006945   PMID:18029348   PMID:18064305   PMID:18093920   PMID:18190591   PMID:18378436   PMID:18386024   PMID:18413760   PMID:18450428   PMID:18450755   PMID:18542065   PMID:18657535  
PMID:18694404   PMID:18957427   PMID:18976975   PMID:18997617   PMID:19010933   PMID:19020713   PMID:19029267   PMID:19056867   PMID:19073610   PMID:19107206   PMID:19126645   PMID:19228696  
PMID:19251947   PMID:19255147   PMID:19305494   PMID:19351365   PMID:19420730   PMID:19450993   PMID:19456850   PMID:19473447   PMID:19581738   PMID:19596856   PMID:19632304   PMID:19661268  
PMID:19696445   PMID:19735958   PMID:19802384   PMID:19822079   PMID:19859083   PMID:19860843   PMID:19866343   PMID:19875451   PMID:20008145   PMID:20013319   PMID:20036233   PMID:20081059  
PMID:20083849   PMID:20097882   PMID:20181947   PMID:20193112   PMID:20200931   PMID:20204274   PMID:20237901   PMID:20307537   PMID:20361982   PMID:20398359   PMID:20430722   PMID:20471559  
PMID:20477813   PMID:20598296   PMID:20683626   PMID:20736897   PMID:20927321   PMID:20971705   PMID:21114861   PMID:21148276   PMID:21257720   PMID:21265098   PMID:21317913   PMID:21320038  
PMID:21327984   PMID:21334435   PMID:21414405   PMID:21430259   PMID:21454203   PMID:21463121   PMID:21623993   PMID:21630196   PMID:21731601   PMID:21757697   PMID:21772125   PMID:21832049  
PMID:21873635   PMID:21886795   PMID:21898481   PMID:21957484   PMID:22024722   PMID:22102278   PMID:22150439   PMID:22237752   PMID:22238310   PMID:22298773   PMID:22308310   PMID:22338054  
PMID:22351752   PMID:22418956   PMID:22573479   PMID:22629140   PMID:22660413   PMID:22672327   PMID:22673509   PMID:22680042   PMID:22686587   PMID:22714920   PMID:22745764   PMID:22766978  
PMID:22899717   PMID:22905270   PMID:22936802   PMID:22939629   PMID:22994707   PMID:23066085   PMID:23144729   PMID:23206733   PMID:23289672   PMID:23331867   PMID:23395182   PMID:23408834  
PMID:23431957   PMID:23504321   PMID:23511033   PMID:23545927   PMID:23546957   PMID:23553620   PMID:23570784   PMID:23576506   PMID:23728345   PMID:23729443   PMID:23824909   PMID:23888783  
PMID:23988031   PMID:23991032   PMID:24029663   PMID:24045542   PMID:24145151   PMID:24222257   PMID:24283919   PMID:24388357   PMID:24392029   PMID:24424718   PMID:24524203   PMID:24529757  
PMID:24549646   PMID:24656090   PMID:24751902   PMID:24762495   PMID:24956062   PMID:24957789   PMID:24970903   PMID:24982376   PMID:25017879   PMID:25063885   PMID:25115297   PMID:25120060  
PMID:25147801   PMID:25198673   PMID:25202019   PMID:25236603   PMID:25267953   PMID:25273930   PMID:25274915   PMID:25321193   PMID:25344834   PMID:25353275   PMID:25361632   PMID:25404732  
PMID:25462564   PMID:25512478   PMID:25589885   PMID:25662098   PMID:25665578   PMID:25732677   PMID:25757215   PMID:25830352   PMID:25891890   PMID:25972509   PMID:26057450   PMID:26076711  
PMID:26191180   PMID:26210886   PMID:26259043   PMID:26289843   PMID:26350464   PMID:26460958   PMID:26513873   PMID:26514209   PMID:26526579   PMID:26561776   PMID:26729247   PMID:26852939  
PMID:26909794   PMID:26953518   PMID:26972718   PMID:27299886   PMID:27305940   PMID:27434331   PMID:27472156   PMID:27556509   PMID:27578500   PMID:27758044   PMID:27819680   PMID:27838471  
PMID:27930836   PMID:28077445   PMID:28107214   PMID:28270211   PMID:28351285   PMID:28382590   PMID:28514442   PMID:28574293   PMID:28579548   PMID:28585128   PMID:28843664   PMID:29212806  
PMID:29216821   PMID:29355516   PMID:29467282   PMID:29484435   PMID:29509190   PMID:29601451   PMID:29628317   PMID:29798960   PMID:29850393   PMID:29905671   PMID:29936329   PMID:29956739  
PMID:29976229   PMID:30065348   PMID:30151336   PMID:30275097   PMID:30379102   PMID:30578753   PMID:30639242   PMID:30679164   PMID:30738694   PMID:30826971   PMID:30918400   PMID:31042409  
PMID:31145753   PMID:31173301   PMID:31327090   PMID:31393853   PMID:31401177   PMID:31439945   PMID:31527615   PMID:31540870   PMID:31543446   PMID:31562188   PMID:31608721   PMID:31619273  
PMID:31622242   PMID:31673058   PMID:31695352   PMID:31797997   PMID:31827001   PMID:31843086   PMID:31976021   PMID:31980649   PMID:32019488   PMID:32046458   PMID:32124938   PMID:32234892  
PMID:32274708   PMID:32274735   PMID:32329146   PMID:32367652   PMID:32388727   PMID:32432735   PMID:32485953   PMID:32530114   PMID:32597227   PMID:32621878   PMID:32623935   PMID:32812461  
PMID:32814053   PMID:32845501   PMID:32897364   PMID:32898003   PMID:32977498   PMID:32978505   PMID:33047116   PMID:33195694   PMID:33197893   PMID:33402482   PMID:33512430   PMID:33567345  
PMID:33595099   PMID:33634586   PMID:33692439   PMID:33741039   PMID:33893369   PMID:33932696   PMID:33961781   PMID:34070901   PMID:34212822   PMID:34343643   PMID:34400721   PMID:34445387  
PMID:34578329   PMID:34590569   PMID:34638892   PMID:34671356   PMID:34699846   PMID:34861818   PMID:34879094   PMID:34990821  


Genomics

Candidate Gene Status
SDC1 is a candidate Gene for QTL BW207_H
SDC1 is a candidate Gene for QTL BW214_H
Comparative Map Data
SDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38220,200,797 - 20,225,475 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl220,200,797 - 20,225,433 (-)EnsemblGRCh38hg38GRCh38
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
T2T-CHM13v2.0220,234,345 - 20,259,019 (-)NCBI
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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2631,562,799 - 31,585,267 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl631,562,739 - 31,585,264 (+)Ensembl
Rnor_6.0633,885,576 - 33,908,038 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl633,885,495 - 33,908,016 (+)EnsemblRnor6.0rn6Rnor6.0
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
(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
CanFam3.11715,220,906 - 15,243,974 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1715,222,094 - 15,243,890 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1715,185,971 - 15,208,368 (-)NCBI
ROS_Cfam_1.01715,373,622 - 15,395,937 (-)NCBI
ROS_Cfam_1.0 Ensembl1715,373,628 - 15,395,946 (-)Ensembl
UMICH_Zoey_3.11715,227,151 - 15,249,524 (-)NCBI
UNSW_CanFamBas_1.01715,233,919 - 15,256,296 (-)NCBI
UU_Cfam_GSD_1.01715,265,578 - 15,287,885 (-)NCBI
Sdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629259,639,887 - 59,661,785 (-)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11487,499,732 - 87,523,122 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1487,499,574 - 87,525,026 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604524,701,281 - 24,725,764 (-)NCBIVero_WHO_p1.0
Sdc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247382,920,154 - 2,938,035 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH67771  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37220,400,635 - 20,400,814UniSTSGRCh37
Build 36220,264,116 - 20,264,295RGDNCBI36
Celera220,262,922 - 20,263,101RGD
Cytogenetic Map2p24.1UniSTS
HuRef220,158,232 - 20,158,411UniSTS
GeneMap99-GB4 RH Map271.85UniSTS
NCBI RH Map299.6UniSTS
RH16622  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37220,401,666 - 20,401,849UniSTSGRCh37
Build 36220,265,147 - 20,265,330RGDNCBI36
Celera220,263,953 - 20,264,136RGD
Cytogenetic Map2p24.1UniSTS
HuRef220,159,263 - 20,159,446UniSTS
GeneMap99-GB4 RH Map271.25UniSTS
NCBI RH Map299.3UniSTS
RH17406  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37220,401,309 - 20,401,466UniSTSGRCh37
Build 36220,264,790 - 20,264,947RGDNCBI36
Celera220,263,596 - 20,263,753RGD
Cytogenetic Map2p24.1UniSTS
HuRef220,158,906 - 20,159,063UniSTS
GeneMap99-GB4 RH Map274.1UniSTS
NCBI RH Map299.6UniSTS

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR10Bhsa-miR-10b-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI22573479
MIR10Bhsa-miR-10b-5pOncomiRDBexternal_infoNANA22573479

Predicted Target Of
Summary Value
Count of predictions:3543
Count of miRNA genes:913
Interacting mature miRNAs:1108
Transcripts:ENST00000254351, ENST00000381150, ENST00000403076, ENST00000429035, ENST00000447124, ENST00000482879
Prediction methods:Microtar, 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.


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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High 5 4 4 3 4 48 21 7 26 13
Medium 952 28 1298 615 594 458 1595 57 171 384 710 1486 170 57 703 4
Low 1234 1550 419 5 667 3 1817 925 2482 14 726 99 4 1 1047 1206 2 2
Below cutoff 248 1395 603 896 1205 1059 17 1 100 865

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_050639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001006946 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_002997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005262620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005262621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005262622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC104792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ551176 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK222739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK299385 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK307313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK311409 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK313974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC008765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM785035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM910157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB321970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J05392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT583891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X60306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z48199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000254351   ⟹   ENSP00000254351
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl220,200,797 - 20,225,130 (-)Ensembl
RefSeq Acc Id: ENST00000381150   ⟹   ENSP00000370542
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl220,200,799 - 20,225,433 (-)Ensembl
RefSeq Acc Id: ENST00000403076   ⟹   ENSP00000384613
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl220,201,486 - 20,225,096 (-)Ensembl
RefSeq Acc Id: ENST00000429035   ⟹   ENSP00000400773
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl220,203,818 - 20,224,280 (-)Ensembl
RefSeq Acc Id: ENST00000447124   ⟹   ENSP00000390201
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl220,204,152 - 20,225,094 (-)Ensembl
RefSeq Acc Id: ENST00000482879
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl220,204,002 - 20,223,388 (-)Ensembl
RefSeq Acc Id: NM_001006946   ⟹   NP_001006947
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38220,200,797 - 20,225,475 (-)NCBI
GRCh37220,400,558 - 20,425,194 (-)ENTREZGENE
Build 36220,264,039 - 20,288,675 (-)NCBI Archive
HuRef220,158,155 - 20,182,491 (-)ENTREZGENE
CHM1_1220,329,922 - 20,354,554 (-)NCBI
T2T-CHM13v2.0220,234,345 - 20,259,019 (-)NCBI
Sequence:
RefSeq Acc Id: NM_002997   ⟹   NP_002988
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38220,200,797 - 20,225,130 (-)NCBI
GRCh37220,400,558 - 20,425,194 (-)ENTREZGENE
Build 36220,264,039 - 20,288,408 (-)NCBI Archive
HuRef220,158,155 - 20,182,491 (-)ENTREZGENE
CHM1_1220,329,922 - 20,354,287 (-)NCBI
T2T-CHM13v2.0220,234,345 - 20,258,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005262620   ⟹   XP_005262677
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38220,200,797 - 20,208,162 (-)NCBI
GRCh37220,400,558 - 20,425,194 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005262621   ⟹   XP_005262678
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38220,200,797 - 20,207,466 (-)NCBI
GRCh37220,400,558 - 20,425,194 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005262622   ⟹   XP_005262679
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38220,200,797 - 20,223,458 (-)NCBI
GRCh37220,400,558 - 20,425,194 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001006947   ⟸   NM_001006946
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: NP_002988   ⟸   NM_002997
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_005262679   ⟸   XM_005262622
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_005262677   ⟸   XM_005262620
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_005262678   ⟸   XM_005262621
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSP00000254351   ⟸   ENST00000254351
RefSeq Acc Id: ENSP00000400773   ⟸   ENST00000429035
RefSeq Acc Id: ENSP00000384613   ⟸   ENST00000403076
RefSeq Acc Id: ENSP00000390201   ⟸   ENST00000447124
RefSeq Acc Id: ENSP00000370542   ⟸   ENST00000381150

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P18827-F1-model_v2 AlphaFold P18827 1-310 view protein structure

Promoters
RGD ID:6859716
Promoter ID:EPDNEW_H3022
Type:initiation region
Name:SDC1_1
Description:syndecan 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3023  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38220,225,130 - 20,225,190EPDNEW
RGD ID:6859718
Promoter ID:EPDNEW_H3023
Type:initiation region
Name:SDC1_2
Description:syndecan 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3022  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38220,225,475 - 20,225,535EPDNEW
RGD ID:6798146
Promoter ID:HG_KWN:31674
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000323932,   UC010EXW.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36220,286,601 - 20,287,427 (-)MPROMDB
RGD ID:6798126
Promoter ID:HG_KWN:31675
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   K562,   Lymphoblastoid
Transcripts:OTTHUMT00000323934
Position:
Human AssemblyChrPosition (strand)Source
Build 36220,287,219 - 20,287,719 (-)MPROMDB
RGD ID:6798125
Promoter ID:HG_KWN:31676
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   Lymphoblastoid,   NB4
Transcripts:NM_001006946,   NM_002997,   OTTHUMT00000323933,   UC010EXV.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36220,288,051 - 20,288,952 (-)MPROMDB
RGD ID:6853472
Promoter ID:EP74561
Type:initiation region
Name:HS_SDC1
Description:Syndecan 1.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Mammalian gene collection (MGC) full-length cDNA cloning
Position:
Human AssemblyChrPosition (strand)Source
Build 36220,288,353 - 20,288,413EPD

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p25.3-23.1(chr2:30141-31766749)x3 copy number gain See cases [RCV000052929] Chr2:30141..31766749 [GRCh38]
Chr2:30141..31991818 [GRCh37]
Chr2:20141..31845322 [NCBI36]
Chr2:2p25.3-23.1
pathogenic
GRCh38/hg38 2p25.3-16.1(chr2:66097-55570637)x3 copy number gain See cases [RCV000052933] Chr2:66097..55570637 [GRCh38]
Chr2:66097..55797773 [GRCh37]
Chr2:56097..55651277 [NCBI36]
Chr2:2p25.3-16.1
pathogenic
NM_001006946.1(SDC1):c.929C>T (p.Ala310Val) single nucleotide variant Malignant melanoma [RCV000065364] Chr2:20202770 [GRCh38]
Chr2:20402531 [GRCh37]
Chr2:20266012 [NCBI36]
Chr2:2p24.1
not provided
NM_001006946.1(SDC1):c.439G>A (p.Glu147Lys) single nucleotide variant Malignant melanoma [RCV000065366] Chr2:20204001 [GRCh38]
Chr2:20403762 [GRCh37]
Chr2:20267243 [NCBI36]
Chr2:2p24.1
not provided
NM_001006946.1(SDC1):c.709C>T (p.Gln237Ter) single nucleotide variant Malignant melanoma [RCV000060460] Chr2:20203141 [GRCh38]
Chr2:20402902 [GRCh37]
Chr2:20266383 [NCBI36]
Chr2:2p24.1
not provided
GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3 copy number gain See cases [RCV000135398] Chr2:30341..28419664 [GRCh38]
Chr2:30341..28642531 [GRCh37]
Chr2:20341..28496035 [NCBI36]
Chr2:2p25.3-23.2
pathogenic
GRCh38/hg38 2p25.3-23.3(chr2:17019-26318846)x3 copy number gain See cases [RCV000137344] Chr2:17019..26318846 [GRCh38]
Chr2:17019..26541714 [GRCh37]
Chr2:7019..26395218 [NCBI36]
Chr2:2p25.3-23.3
pathogenic
GRCh38/hg38 2p25.3-24.1(chr2:1664615-23664142)x3 copy number gain See cases [RCV000137913] Chr2:1664615..23664142 [GRCh38]
Chr2:1668387..23887012 [GRCh37]
Chr2:1647394..23740517 [NCBI36]
Chr2:2p25.3-24.1
pathogenic|likely pathogenic
GRCh38/hg38 2p24.2-24.1(chr2:16723596-21600734)x1 copy number loss See cases [RCV000139451] Chr2:16723596..21600734 [GRCh38]
Chr2:16904863..21823606 [GRCh37]
Chr2:16768344..21677111 [NCBI36]
Chr2:2p24.2-24.1
pathogenic|likely pathogenic
GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3 copy number gain See cases [RCV000141829] Chr2:12770..33711509 [GRCh38]
Chr2:12770..33936576 [GRCh37]
Chr2:2770..33790080 [NCBI36]
Chr2:2p25.3-22.3
pathogenic
GRCh38/hg38 2p25.3-23.3(chr2:12770-25039694)x3 copy number gain See cases [RCV000141877] Chr2:12770..25039694 [GRCh38]
Chr2:12770..25262563 [GRCh37]
Chr2:2770..25116067 [NCBI36]
Chr2:2p25.3-23.3
pathogenic
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2
benign
GRCh38/hg38 2p25.3-21(chr2:236816-45983232)x3 copy number gain See cases [RCV000143682] Chr2:236816..45983232 [GRCh38]
Chr2:236816..46210371 [GRCh37]
Chr2:226816..46063875 [NCBI36]
Chr2:2p25.3-21
pathogenic
NM_002997.5(SDC1):c.188C>T (p.Ser63Phe) single nucleotide variant Long QT syndrome [RCV000190182] Chr2:20204252 [GRCh38]
Chr2:20404013 [GRCh37]
Chr2:2p24.1
likely benign
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) copy number gain See cases [RCV000512056] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 copy number gain See cases [RCV000511212] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p24.1-23.3(chr2:19905995-24762790)x1 copy number loss not provided [RCV000682157] Chr2:19905995..24762790 [GRCh37]
Chr2:2p24.1-23.3
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 copy number gain not provided [RCV000752804] Chr2:15672..243101834 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p24.1(chr2:20423601-20424725)x1 copy number loss not provided [RCV000752871] Chr2:20423601..20424725 [GRCh37]
Chr2:2p24.1
benign
GRCh37/hg19 2p24.1(chr2:20423867-20427189)x1 copy number loss not provided [RCV000752874] Chr2:20423867..20427189 [GRCh37]
Chr2:2p24.1
benign
GRCh37/hg19 2p24.1(chr2:20423488-20424838)x1 copy number loss not provided [RCV000752870] Chr2:20423488..20424838 [GRCh37]
Chr2:2p24.1
benign
GRCh37/hg19 2p24.1(chr2:20423601-20424838)x1 copy number loss not provided [RCV000752872] Chr2:20423601..20424838 [GRCh37]
Chr2:2p24.1
benign
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 copy number gain not provided [RCV000752802] Chr2:14238..243048760 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p24.1(chr2:20423264-20425165)x0 copy number loss not provided [RCV000752868] Chr2:20423264..20425165 [GRCh37]
Chr2:2p24.1
benign
GRCh37/hg19 2p24.1(chr2:20423488-20424725)x1 copy number loss not provided [RCV000752869] Chr2:20423488..20424725 [GRCh37]
Chr2:2p24.1
benign
NM_002997.5(SDC1):c.672C>T (p.Ala224=) single nucleotide variant not provided [RCV000904725] Chr2:20203178 [GRCh38]
Chr2:20402939 [GRCh37]
Chr2:2p24.1
likely benign
NM_002997.5(SDC1):c.576T>C (p.Ala192=) single nucleotide variant not provided [RCV000768080] Chr2:20203864 [GRCh38]
Chr2:20403625 [GRCh37]
Chr2:2p24.1
uncertain significance
NM_002997.5(SDC1):c.203C>T (p.Thr68Met) single nucleotide variant not provided [RCV000973667] Chr2:20204237 [GRCh38]
Chr2:20403998 [GRCh37]
Chr2:2p24.1
benign
NM_002997.5(SDC1):c.346G>A (p.Ala116Thr) single nucleotide variant not provided [RCV000918508] Chr2:20204094 [GRCh38]
Chr2:20403855 [GRCh37]
Chr2:2p24.1
benign
NM_002997.5(SDC1):c.227C>T (p.Thr76Met) single nucleotide variant not provided [RCV000894306] Chr2:20204213 [GRCh38]
Chr2:20403974 [GRCh37]
Chr2:2p24.1
benign
GRCh37/hg19 2p24.3-24.1(chr2:15631145-21729493)x1 copy number loss not provided [RCV000847885] Chr2:15631145..21729493 [GRCh37]
Chr2:2p24.3-24.1
pathogenic
GRCh37/hg19 2p24.1(chr2:20167711-20601004)x3 copy number gain not provided [RCV000848211] Chr2:20167711..20601004 [GRCh37]
Chr2:2p24.1
uncertain significance
NM_002997.5(SDC1):c.312T>C (p.Ala104=) single nucleotide variant not provided [RCV000952820] Chr2:20204128 [GRCh38]
Chr2:20403889 [GRCh37]
Chr2:2p24.1
benign
NM_002997.5(SDC1):c.244G>A (p.Gly82Ser) single nucleotide variant not provided [RCV000888906] Chr2:20204196 [GRCh38]
Chr2:20403957 [GRCh37]
Chr2:2p24.1
benign
NC_000002.11:g.(?_20113319)_(21266817_?)dup duplication Cranioectodermal dysplasia 2 [RCV001883009]|not provided [RCV001900523] Chr2:20113319..21266817 [GRCh37]
Chr2:2p24.1
uncertain significance
GRCh37/hg19 2p24.1(chr2:20421008-20430049)x1 copy number loss not provided [RCV000740350] Chr2:20421008..20430049 [GRCh37]
Chr2:2p24.1
benign
GRCh37/hg19 2p24.1(chr2:20423601-20425165)x1 copy number loss not provided [RCV000752873] Chr2:20423601..20425165 [GRCh37]
Chr2:2p24.1
benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10658 AgrOrtholog
COSMIC SDC1 COSMIC
Ensembl Genes ENSG00000115884 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000254351 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000370542 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000384613 UniProtKB/TrEMBL
  ENSP00000390201 UniProtKB/TrEMBL
  ENSP00000400773 UniProtKB/TrEMBL
Ensembl Transcript ENST00000254351 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000381150 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000403076 UniProtKB/TrEMBL
  ENST00000429035 UniProtKB/TrEMBL
  ENST00000447124 UniProtKB/TrEMBL
GTEx ENSG00000115884 GTEx
HGNC ID HGNC:10658 ENTREZGENE
Human Proteome Map SDC1 Human Proteome Map
InterPro Neurexin-like UniProtKB/Swiss-Prot
  Syndecan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syndecan-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syndecan/Neurexin_dom UniProtKB/Swiss-Prot
  Syndecan_CS UniProtKB/Swiss-Prot
KEGG Report hsa:6382 UniProtKB/Swiss-Prot
NCBI Gene 6382 ENTREZGENE
OMIM 186355 OMIM
PANTHER PTHR10915 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10915:SF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Syndecan UniProtKB/Swiss-Prot
PharmGKB PA35588 PharmGKB
PROSITE SYNDECAN UniProtKB/Swiss-Prot
SMART 4.1m UniProtKB/Swiss-Prot
UniProt E9PHH3_HUMAN UniProtKB/TrEMBL
  F8WCX9_HUMAN UniProtKB/TrEMBL
  H7C1K4_HUMAN UniProtKB/TrEMBL
  P18827 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary D6W523 UniProtKB/Swiss-Prot
  Q53QV0 UniProtKB/Swiss-Prot
  Q546D3 UniProtKB/Swiss-Prot
  Q96HB7 UniProtKB/Swiss-Prot