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

Gene ID: 25992, updated on 5-Aug-2022

Summary

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. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 13.4), gall bladder (RPKM 12.9) and 24 other tissues See more
Orthologs
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Genomic context

See SNED1 in Genome Data Viewer
Location:
2q37.3
Exon count:
36
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (240997650..241095568)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (241497601..241594674)
105.20220307 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 uncharacterized LOC112268440 Neighboring gene up-regulated in colorectal cancer liver metastasis Neighboring gene uncharacterized LOC107985787 Neighboring gene SNED1 antisense RNA 1 Neighboring gene mitochondrial transcription termination factor 4 Neighboring gene PAS domain containing serine/threonine kinase Neighboring gene uncharacterized LOC105373971 Neighboring gene protein phosphatase 1 regulatory subunit 7

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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

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_001080437.3NP_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
    Q8TEP7, Q8TER0
    Related
    ENSP00000308893.8, ENST00000310397.13
    Conserved Domains (4) summary
    smart00539
    Location:104260
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00054
    Location:311347
    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:11061184
    fn3; Fibronectin type III domain
    pfam00084
    Location:698751
    Sushi; Sushi repeat (SCR repeat)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_011510931.3XP_011509233.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X1

    Conserved Domains (4) summary
    smart00539
    Location:128284
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00054
    Location:335371
    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:11301208
    fn3; Fibronectin type III domain
    pfam00084
    Location:722775
    Sushi; Sushi repeat (SCR repeat)
  2. XM_011510932.3XP_011509234.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X2

    Conserved Domains (4) summary
    smart00539
    Location:128284
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00054
    Location:335371
    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:11301208
    fn3; Fibronectin type III domain
    pfam00084
    Location:722775
    Sushi; Sushi repeat (SCR repeat)
  3. XM_047443885.1XP_047299841.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X3

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

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

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

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

    Conserved Domains (5) summary
    smart00539
    Location:128284
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00054
    Location:335371
    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:11281208
    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:9321012
    fn3; Fibronectin type III domain
    pfam00084
    Location:722775
    Sushi; Sushi repeat (SCR repeat)
  8. XM_047443890.1XP_047299846.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X10

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

    Related
    ENSP00000384871.1, ENST00000401884.5
    Conserved Domains (4) summary
    smart00539
    Location:128284
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00054
    Location:335371
    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:11301208
    fn3; Fibronectin type III domain
    pfam00084
    Location:722775
    Sushi; Sushi repeat (SCR repeat)
  10. XM_011510937.3XP_011509239.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X11

    Conserved Domains (3) summary
    smart00539
    Location:128284
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00054
    Location:335371
    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:722775
    Sushi; Sushi repeat (SCR repeat)
  11. XM_047443886.1XP_047299842.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X4

    Related
    ENSP00000386007.3, ENST00000405547.7
  12. XM_047443887.1XP_047299843.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X5

  13. XM_047443889.1XP_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
    241497601..241594674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)