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    SNED1 sushi, nidogen and EGF like domains 1 [ Homo sapiens (human) ]

    Gene ID: 25992, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SNED1provided by HGNC
    Official Full Name
    sushi, nidogen and EGF like domains 1provided by HGNC
    Primary source
    HGNC:HGNC:24696
    See related
    Ensembl:ENSG00000162804 MIM:616634; AllianceGenome:HGNC:24696
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SST3; Snep; IRE-BP1
    Summary
    Predicted to enable Notch binding activity. Predicted to be involved in cell-matrix adhesion. Located in extracellular matrix. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 13.4), gall bladder (RPKM 12.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNED1 in Genome Data Viewer
    Location:
    2q37.3
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (240997650..241095568)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (241496555..241594674)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (241938035..242034983)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ciliary rootlet coiled-coil, rootletin family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241894006-241894576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241897431-241898000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241901185-241902036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241902037-241902887 Neighboring gene up-regulated in colorectal cancer liver metastasis Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241922772-241923279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241923280-241923786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12525 Neighboring gene uncharacterized LOC107985787 Neighboring gene TWIST1 associated long noncoding RNA regulated by androgen receptor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:241949545-241950150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241950151-241950754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241957354-241957854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241957855-241958355 Neighboring gene SNED1 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241973517-241974460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241974461-241975402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:241975403-241976346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12526 Neighboring gene mitochondrial transcription termination factor 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242012857-242013373 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242040949-242041488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242041489-242042028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17415 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57723 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57727 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17417 Neighboring gene PAS domain containing serine/threonine kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242079269-242079769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12529 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242097726-242098226 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:242106157-242106656 Neighboring gene uncharacterized LOC105373971 Neighboring gene protein phosphatase 1 regulatory subunit 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242125644-242126166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242127362-242128046

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome. Vallet SD, et al. Biochem J, 2021 Apr 16. PMID 33724335
    2. Cloning and expression analysis of the mouse stroma marker Snep encoding a novel nidogen domain protein. Leimeister C, et al. Dev Dyn, 2004 Jun. PMID 15162516
    3. Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in postmenopausal women. Prescott J, et al. PLoS One, 2012. PMID 22675492, Free PMC Article
    4. A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response. Roewenstrunk J, et al. Sci Rep, 2019 Apr 12. PMID 30979931, Free PMC Article
    5. LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition. Hu Q, et al. Cell Res, 2019 Apr. PMID 30631154, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in postmenopausal women.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ00133, DKFZp586B2420

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables Notch binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-matrix adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sushi, nidogen and EGF-like domain-containing protein 1
    Names
    insulin responsive sequence DNA binding protein-1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001080437.3 → NP_001073906.1  sushi, nidogen and EGF-like domain-containing protein 1 precursor

      See identical proteins and their annotated locations for NP_001073906.1

      Status: VALIDATED

      Source sequence(s)
      AC005237, AC093585, AC104809, AL050143, KF510803
      Consensus CDS
      CCDS46562.1
      UniProtKB/Swiss-Prot
      B5MDC3, B7WNK6, B7WPM0, Q336F4, Q336F5, Q8N369, Q8TEP7, Q8TER0
      Related
      ENSP00000308893.8, ENST00000310397.13
      Conserved Domains (4) summary
      smart00539
      Location:104 → 260
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      cd00054
      Location:311 → 347
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam00041
      Location:1106 → 1184
      fn3; Fibronectin type III domain
      pfam00084
      Location:698 → 751
      Sushi; Sushi repeat (SCR repeat)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      240997650..241095568
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510931.3 → XP_011509233.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X1

      Conserved Domains (4) summary
      smart00539
      Location:128 → 284
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      cd00054
      Location:335 → 371
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam00041
      Location:1130 → 1208
      fn3; Fibronectin type III domain
      pfam00084
      Location:722 → 775
      Sushi; Sushi repeat (SCR repeat)

    2. XM_011510932.3 → XP_011509234.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X2

      Conserved Domains (4) summary
      smart00539
      Location:128 → 284
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      cd00054
      Location:335 → 371
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam00041
      Location:1130 → 1208
      fn3; Fibronectin type III domain
      pfam00084
      Location:722 → 775
      Sushi; Sushi repeat (SCR repeat)

    3. XM_047443885.1 → XP_047299841.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X3

    4. XM_047443888.1 → XP_047299844.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X6

    5. XM_047443884.1 → XP_047299840.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X1

    6. XM_047443891.1 → XP_047299847.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X10

    7. XM_024452784.2 → XP_024308552.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X7

      Conserved Domains (5) summary
      smart00539
      Location:128 → 284
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      cd00054
      Location:335 → 371
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00063
      Location:1128 → 1208
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:932 → 1012
      fn3; Fibronectin type III domain
      pfam00084
      Location:722 → 775
      Sushi; Sushi repeat (SCR repeat)

    8. XM_047443890.1 → XP_047299846.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X10

    9. XM_011510934.4 → XP_011509236.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X9

      Related
      ENSP00000384871.1, ENST00000401884.5
      Conserved Domains (4) summary
      smart00539
      Location:128 → 284
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      cd00054
      Location:335 → 371
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam00041
      Location:1130 → 1208
      fn3; Fibronectin type III domain
      pfam00084
      Location:722 → 775
      Sushi; Sushi repeat (SCR repeat)

    10. XM_011510937.3 → XP_011509239.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X11

      Conserved Domains (3) summary
      smart00539
      Location:128 → 284
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      cd00054
      Location:335 → 371
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam00084
      Location:722 → 775
      Sushi; Sushi repeat (SCR repeat)

    11. XM_047443886.1 → XP_047299842.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X4

      Related
      ENSP00000386007.3, ENST00000405547.7

    12. XM_047443887.1 → XP_047299843.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X5

    13. XM_047443889.1 → XP_047299845.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X8

    RNA

    1. XR_002959254.2 RNA Sequence

    2. XR_002959256.2 RNA Sequence

    3. XR_002959257.2 RNA Sequence

    4. XR_002959258.2 RNA Sequence

    5. XR_002959262.2 RNA Sequence

    6. XR_007071512.1 RNA Sequence

    7. XR_002959260.2 RNA Sequence

    8. XR_002959255.2 RNA Sequence

    9. XR_002959263.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      241496555..241594674
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341325.1 → XP_054197300.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X7

    2. XM_054341327.1 → XP_054197302.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X9

    3. XM_054341330.1 → XP_054197305.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X11

    4. XM_054341329.1 → XP_054197304.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X10

    5. XM_054341328.1 → XP_054197303.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X10

    6. XM_054341320.1 → XP_054197295.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X2

    7. XM_054341324.1 → XP_054197299.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X6

    8. XM_054341319.1 → XP_054197294.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X1

    9. XM_054341318.1 → XP_054197293.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X1

    10. XM_054341321.1 → XP_054197296.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X3

    11. XM_054341322.1 → XP_054197297.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X4

    12. XM_054341323.1 → XP_054197298.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X5

    13. XM_054341326.1 → XP_054197301.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X8

    RNA

    1. XR_008486315.1 RNA Sequence

    2. XR_008486313.1 RNA Sequence

    3. XR_008486311.1 RNA Sequence

    4. XR_008486314.1 RNA Sequence

    5. XR_008486316.1 RNA Sequence

    6. XR_008486317.1 RNA Sequence

    7. XR_008486318.1 RNA Sequence

    8. XR_008486312.1 RNA Sequence

    9. XR_008486319.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TER0.2 GenPept UniProtKB/Swiss-Prot:Q8TER0

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