SDC4 (syndecan 4) - Rat Genome Database

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Gene: SDC4 (syndecan 4) Homo sapiens
Analyze
Symbol: SDC4
Name: syndecan 4
RGD ID: 730877
HGNC Page HGNC
Description: Enables identical protein binding activity and thrombospondin receptor activity. Involved in negative regulation of T cell proliferation; positive regulation of exosomal secretion; and positive regulation of extracellular exosome assembly. Located in extracellular exosome. Biomarker of myocardial infarction.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: amphiglycan; MGC22217; ryudocan amphiglycan; ryudocan core protein; SYND4; syndecan 4 (amphiglycan, ryudocan); syndecan proteoglycan 4; syndecan-4
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: SDC4P  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
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 (-)NCBINCBI36hg18NCBI36
Build 342043,387,343 - 43,410,478NCBI
Celera2040,662,456 - 40,685,588 (-)NCBI
Cytogenetic Map20q13.12NCBI
HuRef2040,695,444 - 40,718,573 (-)NCBIHuRef
CHM1_12043,856,488 - 43,879,617 (-)NCBICHM1_1
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  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
4,4'-sulfonyldiphenol  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (EXP)
7,12-dimethyltetraphene  (ISO)
acetazolamide  (ISO)
acetylsalicylic acid  (EXP)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (EXP)
ammonium chloride  (ISO)
Apratastat  (EXP)
arsenous acid  (EXP)
atrazine  (EXP)
Benoxacor  (ISO)
benzo[a]pyrene  (EXP)
benzo[a]pyrene diol epoxide I  (EXP)
beta-D-glucosamine  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bleomycin A5  (EXP)
bromobenzene  (ISO)
buspirone  (ISO)
butanal  (EXP)
C60 fullerene  (ISO)
calcidiol  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clofibrate  (ISO)
copper(II) sulfate  (EXP)
corticosterone  (ISO)
Cuprizon  (ISO)
cyclosporin A  (EXP)
cytarabine  (EXP)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (EXP)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dioxygen  (ISO)
dorsomorphin  (EXP)
endosulfan  (ISO)
ethanol  (ISO)
folic acid  (ISO)
furan  (ISO)
gamma-hexachlorocyclohexane  (ISO)
glafenine  (ISO)
graphite  (ISO)
heparin  (EXP)
hydrogen cyanide  (ISO)
hydrogen peroxide  (EXP)
hydroquinone O-beta-D-glucopyranoside  (EXP)
indometacin  (EXP)
irinotecan  (EXP)
kojic acid  (EXP)
L-methionine  (ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
leflunomide  (EXP)
levofloxacin  (ISO)
Licochalcone B  (EXP)
methylmercury chloride  (EXP)
morphine  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (EXP)
nickel dichloride  (EXP)
nickel sulfate  (EXP)
nicotine  (ISO)
nitroglycerin  (ISO)
omega-6 fatty acid  (EXP)
oxaliplatin  (ISO)
panobinostat  (EXP)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (ISO)
permethrin  (ISO)
phenethyl caffeate  (ISO)
phenformin  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (EXP)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
pirinixic acid  (ISO)
potassium cyanide  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (EXP)
propiconazole  (ISO)
quercetin  (EXP)
rac-lactic acid  (EXP)
SB 431542  (EXP)
sevoflurane  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP)
Soman  (ISO)
succimer  (ISO)
sunitinib  (EXP)
temozolomide  (EXP)
testosterone  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
topotecan  (ISO)
trichloroethene  (ISO)
trichostatin A  (EXP)
triphenyl phosphate  (ISO)
Triptolide  (ISO)
tris(2-butoxyethyl) phosphate  (EXP)
troglitazone  (ISO)
tunicamycin  (EXP)
urethane  (EXP)
valproic acid  (EXP)
vinclozolin  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)
zoledronic acid  (EXP)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Additional References at PubMed
PMID:1500433   PMID:7626103   PMID:7690138   PMID:7916598   PMID:8019004   PMID:8125298   PMID:8570206   PMID:8621465   PMID:8797100   PMID:9111037   PMID:9342064   PMID:9556568  
PMID:9582338   PMID:9660868   PMID:10497173   PMID:10911369   PMID:11024024   PMID:11456484   PMID:11549250   PMID:11567105   PMID:11780052   PMID:11801740   PMID:11805099   PMID:11889131  
PMID:11916978   PMID:12011116   PMID:12241528   PMID:12377772   PMID:12477932   PMID:12493766   PMID:12509413   PMID:12571249   PMID:12885232   PMID:14637022   PMID:14652650   PMID:14670076  
PMID:15033938   PMID:15489334   PMID:15572366   PMID:15731100   PMID:15797855   PMID:15819887   PMID:15968398   PMID:16007225   PMID:16087677   PMID:16157597   PMID:16253987   PMID:16319082  
PMID:16636895   PMID:16817962   PMID:16822948   PMID:16934308   PMID:16982797   PMID:17545042   PMID:17870067   PMID:17879962   PMID:17901052   PMID:18029348   PMID:18093920   PMID:18158320  
PMID:18342939   PMID:18499669   PMID:18638267   PMID:18775505   PMID:19199708   PMID:19322201   PMID:19350579   PMID:19519784   PMID:19538537   PMID:19632304   PMID:19684582   PMID:19695308  
PMID:19696445   PMID:19821490   PMID:19822079   PMID:19875451   PMID:19913121   PMID:20229236   PMID:20398359   PMID:20485444   PMID:20607801   PMID:20628086   PMID:20639201   PMID:20929862  
PMID:20953189   PMID:21036168   PMID:21114861   PMID:21252093   PMID:21414405   PMID:21430259   PMID:21482826   PMID:21873635   PMID:21949132   PMID:21988832   PMID:22164265   PMID:22268118  
PMID:22351752   PMID:22531343   PMID:22569333   PMID:22623531   PMID:22660413   PMID:22721673   PMID:22898364   PMID:23374111   PMID:23374155   PMID:23376485   PMID:23499501   PMID:23525101  
PMID:23576453   PMID:23844358   PMID:23948417   PMID:24558194   PMID:24632200   PMID:24942878   PMID:24956062   PMID:25122554   PMID:25202019   PMID:25216363   PMID:25361632   PMID:25404299  
PMID:25410619   PMID:25416956   PMID:25449226   PMID:26160374   PMID:26186194   PMID:26254886   PMID:26261514   PMID:26350464   PMID:26496610   PMID:26561776   PMID:26760575   PMID:26796346  
PMID:26972000   PMID:27041028   PMID:27279133   PMID:27279134   PMID:27448535   PMID:27541034   PMID:27591995   PMID:27662820   PMID:28077445   PMID:28190767   PMID:28514442   PMID:28703800  
PMID:29016732   PMID:29121646   PMID:29232393   PMID:29467282   PMID:30165731   PMID:30278359   PMID:30282023   PMID:30370584   PMID:30471916   PMID:30963564   PMID:30967474   PMID:31111299  
PMID:31309562   PMID:31495068   PMID:31527615   PMID:31907416   PMID:31980649   PMID:32269093   PMID:32296183   PMID:32315719   PMID:32321914   PMID:33246160   PMID:33545068   PMID:33721368  
PMID:33961781   PMID:34020743   PMID:34029877   PMID:34058069   PMID:34069441   PMID:34180077   PMID:34374198   PMID:34445387   PMID:34790051   PMID:35054983  


Genomics

Comparative Map Data
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 (-)NCBINCBI36hg18NCBI36
Build 342043,387,343 - 43,410,478NCBI
Celera2040,662,456 - 40,685,588 (-)NCBI
Cytogenetic Map20q13.12NCBI
HuRef2040,695,444 - 40,718,573 (-)NCBIHuRef
CHM1_12043,856,488 - 43,879,617 (-)NCBICHM1_1
Sdc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392164,266,167 - 164,285,512 (-)NCBIGRCm39mm39
GRCm39 Ensembl2164,266,167 - 164,285,807 (-)Ensembl
GRCm382164,424,247 - 164,443,188 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2164,424,247 - 164,443,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv372164,249,747 - 164,268,688 (-)NCBIGRCm37mm9NCBIm37
MGSCv362164,115,452 - 164,134,393 (-)NCBImm8
Celera2170,361,365 - 170,380,306 (-)NCBICelera
Cytogenetic Map2H3NCBI
cM Map285.16NCBI
Sdc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23153,154,888 - 153,173,576 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3153,154,896 - 153,173,580 (-)Ensembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13155,352,182 - 155,370,861 (-)NCBI
Celera3151,766,226 - 151,784,912 (-)NCBICelera
Cytogenetic Map3q42NCBI
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_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 (-)NCBI
ROS_Cfam_1.02433,339,093 - 33,359,207 (-)NCBI
ROS_Cfam_1.0 Ensembl2433,339,093 - 33,359,179 (-)Ensembl
UMICH_Zoey_3.12432,600,350 - 32,620,457 (-)NCBI
UNSW_CanFamBas_1.02432,715,919 - 32,736,026 (-)NCBI
UU_Cfam_GSD_1.02433,259,679 - 33,280,258 (-)NCBI
Sdc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640192,074,895 - 192,108,750 (+)NCBI
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 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl218,490,485 - 18,513,332 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605067,132,278 - 67,155,156 (+)NCBIVero_WHO_p1.0
Sdc4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247909,146,371 - 9,166,729 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
G43350  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372043,973,780 - 43,973,929UniSTSGRCh37
Build 362043,407,194 - 43,407,343RGDNCBI36
Celera2040,682,306 - 40,682,455RGD
Cytogenetic Map20q12UniSTS
HuRef2040,715,289 - 40,715,438UniSTS
RH102672  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372043,973,873 - 43,974,044UniSTSGRCh37
Build 362043,407,287 - 43,407,458RGDNCBI36
Celera2040,682,399 - 40,682,570RGD
Cytogenetic Map20q12UniSTS
HuRef2040,715,382 - 40,715,553UniSTS
GeneMap99-GB4 RH Map20237.62UniSTS
G54026  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372043,954,307 - 43,954,446UniSTSGRCh37
Build 362043,387,721 - 43,387,860RGDNCBI36
Celera2040,662,835 - 40,662,974RGD
Cytogenetic Map20q12UniSTS
HuRef2040,695,824 - 40,695,963UniSTS
G59912  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372043,973,810 - 43,973,916UniSTSGRCh37
Build 362043,407,224 - 43,407,330RGDNCBI36
Celera2040,682,336 - 40,682,442RGD
Cytogenetic Map20q12UniSTS
HuRef2040,715,319 - 40,715,425UniSTS
TNG Radiation Hybrid Map2015669.0UniSTS
SDC4_251  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372043,953,898 - 43,954,784UniSTSGRCh37
Build 362043,387,312 - 43,388,198RGDNCBI36
Celera2040,662,426 - 40,663,312RGD
HuRef2040,695,414 - 40,696,301UniSTS
WI-11633  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372043,953,969 - 43,954,068UniSTSGRCh37
Build 362043,387,383 - 43,387,482RGDNCBI36
Celera2040,662,497 - 40,662,596RGD
Cytogenetic Map20q12UniSTS
HuRef2040,695,485 - 40,695,584UniSTS
GeneMap99-GB4 RH Map20290.27UniSTS
GeneMap99-GB4 RH Map20237.11UniSTS
Whitehead-RH Map20292.7UniSTS
NCBI RH Map20469.1UniSTS
RH48325  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372043,958,516 - 43,958,640UniSTSGRCh37
Build 362043,391,930 - 43,392,054RGDNCBI36
Celera2040,667,043 - 40,667,167RGD
Cytogenetic Map20q12UniSTS
HuRef2040,700,030 - 40,700,154UniSTS
GeneMap99-GB4 RH Map20255.13UniSTS
WI-7527  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372043,954,824 - 43,955,172UniSTSGRCh37
Build 362043,388,238 - 43,388,586RGDNCBI36
Celera2040,663,352 - 40,663,699RGD
Cytogenetic Map20q12UniSTS
HuRef2040,696,341 - 40,696,685UniSTS
GeneMap99-GB4 RH Map20254.92UniSTS
Whitehead-YAC Contig Map20 UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1205
Count of miRNA genes:594
Interacting mature miRNAs:671
Transcripts:ENST00000372733, ENST00000537976
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.


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 6 1 26 9 8 8 26 31 43 4 3
Medium 2429 2228 1695 614 829 456 4347 2140 3484 392 1425 1549 171 1 1204 2784 6 2
Low 3 751 5 1 984 1 2 52 246 1 3 18 1
Below cutoff 1 9 93 4 4 1 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_002999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011528977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AK222695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK223243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK303964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK312507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL021578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC030805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR542045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR542074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D13292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D79206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT584003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U36599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X67016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000372733   ⟹   ENSP00000361818
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2045,325,288 - 45,348,424 (-)Ensembl
RefSeq Acc Id: NM_002999   ⟹   NP_002990
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,325,288 - 45,348,424 (-)NCBI
GRCh372043,953,928 - 43,977,064 (-)ENTREZGENE
GRCh372043,953,928 - 43,977,064 (-)NCBI
Build 362043,387,342 - 43,410,478 (-)NCBI Archive
HuRef2040,695,444 - 40,718,573 (-)ENTREZGENE
CHM1_12043,856,488 - 43,879,617 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011528977   ⟹   XP_011527279
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,325,288 - 45,348,424 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_002990   ⟸   NM_002999
- Peptide Label: precursor
- UniProtKB: P31431 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011527279   ⟸   XM_011528977
- Peptide Label: isoform X1
- UniProtKB: B4E1S6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000361818   ⟸   ENST00000372733
Protein Domains
4.1m

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P31431-F1-model_v2 AlphaFold P31431 1-198 view protein structure

Promoters
RGD ID:6799047
Promoter ID:HG_KWN:39588
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000080515
Position:
Human AssemblyChrPosition (strand)Source
Build 362043,410,176 - 43,410,676 (-)MPROMDB
RGD ID:13207049
Promoter ID:EPDNEW_H27105
Type:initiation region
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:
Human AssemblyChrPosition (strand)Source
GRCh382045,348,424 - 45,348,484EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33
pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33
pathogenic
GRCh38/hg38 20q13.12(chr20:45304962-45374661)x3 copy number gain See cases [RCV000135905] Chr20:45304962..45374661 [GRCh38]
Chr20:43933602..44003301 [GRCh37]
Chr20:43367016..43436715 [NCBI36]
Chr20:20q13.12
benign
GRCh38/hg38 20q11.22-13.12(chr20:35237946-47631818)x1 copy number loss See cases [RCV000140816] Chr20:35237946..47631818 [GRCh38]
Chr20:33825749..46260562 [GRCh37]
Chr20:33289165..45693969 [NCBI36]
Chr20:20q11.22-13.12
pathogenic
GRCh37/hg19 20q13.12(chr20:43955980-44053178)x3 copy number gain Ductal breast carcinoma [RCV000207186] Chr20:43955980..44053178 [GRCh37]
Chr20:20q13.12
uncertain significance
NM_002999.4(SDC4):c.446-1455C>T single nucleotide variant Type 2 diabetes mellitus [RCV000626342] Chr20:45328870 [GRCh38]
Chr20:43957510 [GRCh37]
Chr20:20q13.12
benign
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)x3 copy number gain See cases [RCV000510832] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33
pathogenic
NM_002999.4(SDC4):c.61-965T>C single nucleotide variant Type 2 diabetes mellitus [RCV000626345] Chr20:45336885 [GRCh38]
Chr20:43965525 [GRCh37]
Chr20:20q13.12
benign
NM_002999.4(SDC4):c.445+251C>T single nucleotide variant Type 2 diabetes mellitus [RCV000626347] Chr20:45330115 [GRCh38]
Chr20:43958755 [GRCh37]
Chr20:20q13.12
benign
NM_002999.4(SDC4):c.199+134A>G single nucleotide variant Type 2 diabetes mellitus [RCV000626349] Chr20:45335648 [GRCh38]
Chr20:43964288 [GRCh37]
Chr20:20q13.12
benign
NM_002999.4(SDC4):c.61-4447del deletion Type 2 diabetes mellitus [RCV000626351] Chr20:45340367 [GRCh38]
Chr20:43969007 [GRCh37]
Chr20:20q13.12
benign
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555) copy number gain See cases [RCV000512450] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33
pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62948788)x3 copy number gain not provided [RCV000741058] Chr20:63244..62948788 [GRCh37]
Chr20:20p13-q13.33
pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62961294)x3 copy number gain not provided [RCV000741059] Chr20:63244..62961294 [GRCh37]
Chr20:20p13-q13.33
pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62912463)x3 copy number gain not provided [RCV000741057] Chr20:63244..62912463 [GRCh37]
Chr20:20p13-q13.33
pathogenic
Single allele deletion Focal-onset seizure [RCV001004039] Chr20:34980430..46806549 [GRCh37]
Chr20:20q11.23-13.13
likely pathogenic
GRCh37/hg19 20q13.12-13.13(chr20:42985044-48599046)x1 copy number loss Developmental and epileptic encephalopathy, 26 [RCV001801198] Chr20:42985044..48599046 [GRCh37]
Chr20:20q13.12-13.13
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10661 AgrOrtholog
COSMIC SDC4 COSMIC
Ensembl Genes ENSG00000124145 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000361818 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000372733 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000124145 GTEx
HGNC ID HGNC:10661 ENTREZGENE
Human Proteome Map SDC4 Human Proteome Map
InterPro Neurexin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syndecan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syndecan/Neurexin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syndecan_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:6385 UniProtKB/Swiss-Prot
NCBI Gene 6385 ENTREZGENE
OMIM 600017 OMIM
PANTHER PTHR10915 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Syndecan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA35591 PharmGKB
PROSITE SYNDECAN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART 4.1m UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B4E1S6 ENTREZGENE, UniProtKB/TrEMBL
  P31431 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O00773 UniProtKB/Swiss-Prot
  Q16833 UniProtKB/Swiss-Prot
  Q53FN9 UniProtKB/Swiss-Prot
  Q6FGN3 UniProtKB/Swiss-Prot