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

Gene ID: 25992, updated on 27-Nov-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, Nov 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: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 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 Variation Viewer (GRCh37.p13)

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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