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Aliases for SNED1 Gene

Aliases for SNED1 Gene

  • Sushi, Nidogen And EGF Like Domains 1 2 3 5
  • IRE-BP1 3 4
  • Sushi, Nidogen And EGF-Like Domain-Containing Protein 1 3
  • Insulin Responsive Sequence DNA Binding Protein-1 3
  • Insulin-Responsive Sequence DNA-Binding Protein 1 4
  • Sushi, Nidogen And EGF-Like Domains 1 2
  • 6720455I24Rik Homolog 3
  • SST3 3
  • Snep 3

External Ids for SNED1 Gene

Previous GeneCards Identifiers for SNED1 Gene

  • GC02P241658
  • GC02P241586
  • GC02P241938
  • GC02P233694

Summaries for SNED1 Gene

GeneCards Summary for SNED1 Gene

SNED1 (Sushi, Nidogen And EGF Like Domains 1) is a Protein Coding gene. Diseases associated with SNED1 include Cortical Thymoma. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is NOTCH3.

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNED1 Gene

Genomics for SNED1 Gene

Regulatory Elements for SNED1 Gene

Enhancers for SNED1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G241616 1.2 ENCODE dbSUPER 38.4 +621.4 621410 4.1 HDGF PKNOX1 GLI4 YY1 ETS1 ZNF143 FOS SP3 YY2 TSHZ1 SNED1 ENSG00000223374 ENSG00000235351 BOK ING5 DTYMK LOC100422094 PASK PPP1R7 FARP2
GH02G240680 0.9 dbSUPER 40.1 -316.3 -316307 0.7 HDGF PKNOX1 GLI4 FOS SP3 YY2 TSHZ1 ZNF662 SMARCA4 ZNF658 SNED1 ENSG00000223374 CAPN10-AS1 LOC100422094 FARP2 AQP12B LOC100420500
GH02G240920 1.9 FANTOM5 Ensembl ENCODE dbSUPER 13.4 -73.8 -73810 6.6 HDGF PKNOX1 ARNT YBX1 ZNF2 ZBTB7B TCF12 ZNF121 GLIS2 ZNF207 CAPN10-AS1 ENSG00000235351 LOC100422094 SNED1 FARP2 ENSG00000223374 DTYMK LOC200772 C2orf54 GPC1
GH02G240603 1.6 Ensembl ENCODE dbSUPER 10.4 -392.3 -392262 3.1 HDGF PKNOX1 FOXA2 ARNT MLX ARID4B DMAP1 YBX1 ZNF2 SLC30A9 CAPN10-AS1 ENSG00000223374 LOC100422094 SNED1 CAPN10 GPR35
GH02G241543 1.3 Ensembl ENCODE 12.3 +548.6 548605 4.4 HDGF PKNOX1 ZNF133 ARID4B YBX1 ZNF2 ZNF48 ZNF121 ZNF766 FOS CAPN10-AS1 ENSG00000223374 BOK RTP5 SNED1 LOC100422094 SEPT2 ENSG00000235351 LOC105373974 STK25
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SNED1 on UCSC Golden Path with GeneCards custom track

Promoters for SNED1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000133215 1303 1401 TBP RB1 ZFP64 SIN3A DMAP1 RAD21 GLIS2 SCRT2 EGR2 SP3

Transcription factor binding sites by QIAGEN in the SNED1 gene promoter:

Genomic Location for SNED1 Gene

Chromosome:
2
Start:
240,997,597 bp from pter
End:
241,095,568 bp from pter
Size:
97,972 bases
Orientation:
Plus strand

Genomic View for SNED1 Gene

Genes around SNED1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNED1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNED1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNED1 Gene

Proteins for SNED1 Gene

  • Protein details for SNED1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TER0-SNED1_HUMAN
    Recommended name:
    Sushi, nidogen and EGF-like domain-containing protein 1
    Protein Accession:
    Q8TER0
    Secondary Accessions:
    • B5MDC3
    • B7WNK6
    • B7WPM0
    • Q336F4
    • Q336F5
    • Q8N369
    • Q8TEP7

    Protein attributes for SNED1 Gene

    Size:
    1413 amino acids
    Molecular mass:
    152204 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH27939.1; Type=Miscellaneous discrepancy; Note=Intron retention. The N-terminal region arises from intron retention.; Evidence={ECO:0000305}; Sequence=AAQ04558.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SNED1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SNED1 Gene

Post-translational modifications for SNED1 Gene

  • Glycosylation at isoforms=3, 4, 5145, isoforms=3, 4, 5408, isoforms=3, 4, 5977, and isoforms=3, 4, 51247
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SNED1 Gene

Domains & Families for SNED1 Gene

Suggested Antigen Peptide Sequences for SNED1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SNED1: view

No data available for UniProtKB/Swiss-Prot for SNED1 Gene

Function for SNED1 Gene

Gene Ontology (GO) - Molecular Function for SNED1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with SNED1: view

Phenotypes for SNED1 Gene

genes like me logo Genes that share phenotypes with SNED1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SNED1

CRISPR Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SNED1 Gene

Localization for SNED1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNED1 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SNED1 gene
Compartment Confidence
extracellular 5
plasma membrane 4
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SNED1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with SNED1: view

Pathways & Interactions for SNED1 Gene

SuperPathways for SNED1 Gene

No Data Available

Interacting Proteins for SNED1 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000308893%0d%0a9606.ENSP00000358795%0d%0a9606.ENSP00000358815%0d%0a9606.ENSP00000282493%0d%0a9606.ENSP00000361467%0d%0a9606.ENSP00000360200%0d%0a
Selected Interacting proteins: Q8TER0-SNED1_HUMAN ENSP00000308893 for SNED1 Gene via IID STRING

Gene Ontology (GO) - Biological Process for SNED1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007160 cell-matrix adhesion IEA --
genes like me logo Genes that share ontologies with SNED1: view

No data available for Pathways by source and SIGNOR curated interactions for SNED1 Gene

Drugs & Compounds for SNED1 Gene

(1) Drugs for SNED1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SNED1: view

Transcripts for SNED1 Gene

Unigene Clusters for SNED1 Gene

Sushi, nidogen and EGF-like domains 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SNED1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20
SP1: - -
SP2:
SP3: -
SP4:
SP5:

Relevant External Links for SNED1 Gene

GeneLoc Exon Structure for
SNED1
ECgene alternative splicing isoforms for
SNED1

Expression for SNED1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNED1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SNED1 Gene

This gene is overexpressed in Serum (63.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SNED1 Gene



NURSA nuclear receptor signaling pathways regulating expression of SNED1 Gene:

SNED1

SOURCE GeneReport for Unigene cluster for SNED1 Gene:

Hs.471834

Evidence on tissue expression from TISSUES for SNED1 Gene

  • Lung(4.3)
  • Spleen(4.2)
  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with SNED1: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNED1 Gene

Orthologs for SNED1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SNED1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SNED1 34 35
  • 98.82 (n)
dog
(Canis familiaris)
Mammalia SNED1 35 34
  • 85.07 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sned1 34
  • 84.21 (n)
mouse
(Mus musculus)
Mammalia Sned1 16 35 34
  • 84.04 (n)
cow
(Bos Taurus)
Mammalia SNED1 35
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SNED1 35
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SNED1 35
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves SNED1 35 34
  • 74.19 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SNED1 35
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sned1 34
  • 58.2 (n)
zebrafish
(Danio rerio)
Actinopterygii sned1 34 35
  • 57.34 (n)
fruit fly
(Drosophila melanogaster)
Insecta C901 35
  • 23 (a)
ManyToMany
uif 35
  • 9 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea lin-12 35
  • 15 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 30 (a)
ManyToMany
Species where no ortholog for SNED1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SNED1 Gene

ENSEMBL:
Gene Tree for SNED1 (if available)
TreeFam:
Gene Tree for SNED1 (if available)

Paralogs for SNED1 Gene

Pseudogenes.org Pseudogenes for SNED1 Gene

genes like me logo Genes that share paralogs with SNED1: view

Variants for SNED1 Gene

Sequence variations from dbSNP and Humsavar for SNED1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000015077 -- 241,076,422(+) TTCCT(G/T)ATTAT intron-variant
rs1000028502 -- 241,033,281(+) ACGCT(G/T)CCTGC intron-variant
rs1000081873 -- 241,032,936(+) TTTTC(A/T)CATTG intron-variant
rs1000107414 -- 241,090,887(+) AAAGA(A/G)AAAAG intron-variant
rs1000165938 -- 240,999,539(+) CCCTT(C/G)CCCAG intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for SNED1 Gene

Variant ID Type Subtype PubMed ID
dgv1222e212 CNV loss 25503493
dgv2194n106 CNV deletion 24896259
dgv772e199 CNV deletion 23128226
esv1359552 CNV insertion 17803354
esv1654437 CNV insertion 17803354
esv2077609 CNV deletion 18987734
esv2200022 CNV deletion 18987734
esv2675882 CNV deletion 23128226
esv2721965 CNV deletion 23290073
esv2721966 CNV deletion 23290073
esv2721967 CNV deletion 23290073
esv2721968 CNV deletion 23290073
esv2721969 CNV deletion 23290073
esv2721970 CNV deletion 23290073
esv2721971 CNV deletion 23290073
esv2721972 CNV deletion 23290073
esv3575345 CNV gain 25503493
esv3584392 CNV loss 25503493
esv3584396 CNV loss 25503493
esv3594813 CNV loss 21293372
esv3594816 CNV loss 21293372
esv3594817 CNV loss 21293372
nsv1072510 CNV deletion 25765185
nsv1125217 CNV insertion 24896259
nsv1140156 CNV insertion 24896259
nsv1144929 CNV deletion 24896259
nsv213970 CNV deletion 16902084
nsv460167 CNV gain 19166990
nsv472069 CNV novel sequence insertion 20440878
nsv584861 CNV gain 21841781
nsv584940 CNV loss 21841781
nsv584954 CNV loss 21841781
nsv955297 CNV deletion 24416366
nsv955298 CNV deletion 24416366

Variation tolerance for SNED1 Gene

Residual Variation Intolerance Score: 9.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.86; 94.83% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SNED1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNED1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNED1 Gene

Disorders for SNED1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SNED1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
cortical thymoma
  • polygonal cell thymoma
- elite association - COSMIC cancer census association via MalaCards
Search SNED1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SNED1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SNED1
genes like me logo Genes that share disorders with SNED1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SNED1 Gene

Publications for SNED1 Gene

  1. Cloning and expression analysis of the mouse stroma marker Snep encoding a novel nidogen domain protein. (PMID: 15162516) Leimeister C. … Gessler M. (Dev. Dyn. 2004) 2 3 64
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 2 3 64
  3. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M. … Moll S. (J Proteomics 2013) 3 64
  4. Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in postmenopausal women. (PMID: 22675492) Prescott J. … De Vivo I. (PLoS ONE 2012) 3 64
  5. Anxiolytic and antidepressant actions of somatostatin: the role of sst2 and sst3 receptors. (PMID: 19609508) Engin E. … Treit D. (Psychopharmacology (Berl.) 2009) 22 64

Products for SNED1 Gene

Sources for SNED1 Gene

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