Aliases for SNED1 Gene

Aliases for SNED1 Gene

  • Sushi, Nidogen And EGF Like Domains 1 2 3 5
  • Sushi, Nidogen And EGF-Like Domain-Containing Protein 1 3 4
  • IRE-BP1 3 4
  • SST3 2 3
  • Snep 2 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
  • FLJ00133 2
  • SNED1 5

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 and Hyperpituitarism. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is NOTCH1.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SNED1 Gene

Genomics for SNED1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SNED1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SNED1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SNED1

Top Transcription factor binding sites by QIAGEN in the SNED1 gene promoter:
  • AML1a

Genomic Locations for SNED1 Gene

Latest Assembly
chr2:240,997,410-241,095,568
(GRCh38/hg38)
Size:
98,159 bases
Orientation:
Plus strand

Previous Assembly
chr2:241,938,035-242,034,983
(GRCh37/hg19 by Entrez Gene)
Size:
96,949 bases
Orientation:
Plus strand

chr2:241,938,255-242,034,983
(GRCh37/hg19 by Ensembl)
Size:
96,729 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 Asn145, Asn408, Asn977, and Ser1247
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SNED1 Gene

Domains & Families for SNED1 Gene

Gene Families for SNED1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for SNED1 Gene

InterPro:
Blocks:
  • Aspartic acid and asparagine hydroxylation site
  • EGF-like calcium-binding
  • Nidogen, extracellular region
ProtoNet:

Suggested Antigen Peptide Sequences for SNED1 Gene

GenScript: Design optimal peptide antigens:
  • Insulin-responsive sequence DNA-binding protein 1 (SNED1_HUMAN)
genes like me logo Genes that share domains with SNED1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SNED1 Gene

Function for SNED1 Gene

Phenotypes From GWAS Catalog for SNED1 Gene

Gene Ontology (GO) - Molecular Function for SNED1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005112 Notch binding IBA 21873635
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with SNED1: view
genes like me logo Genes that share phenotypes with SNED1: view

Animal Models for research

  • Taconic Biosciences Mouse Models for SNED1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNED1

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 4
plasma membrane 3
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for SNED1 Gene

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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SNED1 Gene

Pathways & Interactions for SNED1 Gene

PathCards logo

SuperPathways for SNED1 Gene

No Data Available

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

mRNA/cDNA for SNED1 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNED1

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

Expression for SNED1 Gene

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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SNED1

SOURCE GeneReport for Unigene cluster for SNED1 Gene:

Hs.471834

Evidence on tissue expression from TISSUES for SNED1 Gene

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

Primer products for research

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 30 31
  • 98.82 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SNED1 30 31
  • 85.07 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sned1 30
  • 84.21 (n)
Mouse
(Mus musculus)
Mammalia Sned1 30 17 31
  • 84.04 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SNED1 31
  • 81 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SNED1 31
  • 71 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SNED1 31
  • 70 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SNED1 30 31
  • 74.19 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SNED1 31
  • 68 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sned1 30
  • 58.2 (n)
Zebrafish
(Danio rerio)
Actinopterygii sned1 30 31
  • 57.34 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta C901 31
  • 23 (a)
ManyToMany
uif 31
  • 9 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea lin-12 31
  • 15 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 30 (a)
ManyToMany
Species where no ortholog for SNED1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SNED1: view image

Paralogs for SNED1 Gene

(26) SIMAP similar genes for SNED1 Gene using alignment to 5 proteins:

  • SNED1_HUMAN
  • B5MEF5_HUMAN
  • H7BYY9_HUMAN
  • H7C0D4_HUMAN
  • H7C1R9_HUMAN

Pseudogenes.org Pseudogenes for SNED1 Gene

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

Variants for SNED1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SNED1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs139139954 Benign: not provided 241,037,292(+) C/T
NM_001080437.3(SNED1):c.984C>T (p.His328=)
SYNONYMOUS
rs1553548453 Not Provided: not provided 240,999,044(+) A/ACT
NM_001080437.3(SNED1):c.208_209CT[3] (p.Tyr71fs)
FRAMESHIFT
rs186778143 Benign: not provided 241,070,110(+) G/A
NM_001080437.3(SNED1):c.3498G>A (p.Pro1166=)
SYNONYMOUS
rs376157092 Likely Benign: not provided 241,082,272(+) C/T
NM_001080437.3(SNED1):c.4034-5C>T
INTRON
rs59269476 Benign: not provided 241,040,361(+) G/T
NM_001080437.3(SNED1):c.1221G>T (p.Gly407=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SNED1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for SNED1 Gene

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

SNP Genotyping and Copy Number Assays for research

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

Disorders for SNED1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SNED1 Gene - From: COP

Disorder Aliases PubMed IDs
cortical thymoma
  • polygonal cell thymoma
hyperpituitarism
growth hormone secreting pituitary adenoma
  • growth hormone producing adenoma of the pituitary
meningioma, familial
  • meningioma, familial, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search SNED1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 (Developmental dynamics : an official publication of the American Association of Anatomists 2004) 2 3
  2. A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response. (PMID: 30979931) Roewenstrunk J … de la Luna S (Scientific reports 2019) 3
  3. LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition. (PMID: 30631154) Hu Q … Yang L (Cell research 2019) 3
  4. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M … Moll S (Journal of proteomics 2013) 3
  5. 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

Products for SNED1 Gene

Sources for SNED1 Gene