Sned1 sushi, nidogen and EGF-like domains 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sned1provided by RGD
Official Full Name: sushi, nidogen and EGF-like domains 1provided by RGD
Primary source: RGD:1566079
See related: EnsemblRapid:ENSRNOG00000023548 AllianceGenome:RGD:1566079
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: IRE-BP1
Summary: Predicted to enable Notch binding activity. Predicted to be involved in cell-matrix adhesion. Predicted to be located in extracellular matrix. Orthologous to human SNED1 (sushi, nidogen and EGF like domains 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 115.6), Kidney (RPKM 96.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q36

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (101221497..101281401)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (93774087..93834003)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (100380487..100439125)

Chromosome 9 - NC_086027.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Increased gene transcription mediated through IRE-BP1 may contribute to beta-cell dysfunction in insulin resistance, and allow for the hypothesis that IRE-BP1 plays a role in the pathophysiology of type 2 diabetes.
Title: Transgenic expression of insulin-response element binding protein-1 in beta-cells reproduces type 2 diabetes.
study supports the notion that IRE-BP1 may be relevant to the action of insulin in vivo and may play a role in the development of insulin resistance and diabetes
Title: Regulation of insulin-response element binding protein-1 in obesity and diabetes: potential role in impaired insulin-induced gene transcription.
stable constitutive expression of IRE-BP1 enhanced glucose transporter expression, glucose uptake, and glycogen accumulation
Title: An insulin-response element-binding protein that ameliorates hyperglycemia in diabetes.
identified a novel transcription factor,insulin-response element-binding protein 1, that binds and transactivates the insulin-response elements of the insulin-like growth factor-binding protein-3 and other insulin responsive genes
Title: Insulin-response element-binding protein 1: a novel Akt substrate involved in transcriptional action of insulin.

Submit: New GeneRIF Correction

General gene information

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Markers

BI290549 (e-PCR)
- UniSTS:244019

RH134511 (e-PCR)
- UniSTS:217791

Gene Ontology Provided by RGD

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	IEA Inferred from Electronic Annotation more info
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
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)

NM_001413841.2 → NP_001400770.1 sushi, nidogen and EGF-like domain-containing protein 1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

Q336F3, Q5ZQU0

UniProtKB/TrEMBL

A6JQY0, D3ZNR4

Related

ENSRNOP00000022290.7, ENSRNOT00000022290.8

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

101221497..101281401

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039083766.2 → XP_038939694.1 sushi, nidogen and EGF-like domain-containing protein 1 isoform X2

UniProtKB/TrEMBL

A6JQY0, D3ZNR4

Conserved Domains (5) summary

cd00033
Location:698 → 752

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

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 ...

cd00063
Location:1205 → 1297

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:1009 → 1089

fn3; Fibronectin type III domain
XM_063267325.1 → XP_063123395.1 sushi, nidogen and EGF-like domain-containing protein 1 isoform X4
XM_039083769.2 → XP_038939697.1 sushi, nidogen and EGF-like domain-containing protein 1 isoform X5

UniProtKB/TrEMBL

A6JQY1

Conserved Domains (3) summary

cd00033
Location:698 → 752

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

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 ...
XM_063267326.1 → XP_063123396.1 sushi, nidogen and EGF-like domain-containing protein 1 isoform X6

UniProtKB/TrEMBL

A6JQY1
XM_039083765.2 → XP_038939693.1 sushi, nidogen and EGF-like domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

A6JQY0, D3ZNR4

Related

ENSRNOP00000112793.1, ENSRNOT00000147153.1

Conserved Domains (5) summary

cd00033
Location:698 → 752

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

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 ...

cd00063
Location:1205 → 1297

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:1009 → 1089

fn3; Fibronectin type III domain
XM_039083768.2 → XP_038939696.1 sushi, nidogen and EGF-like domain-containing protein 1 isoform X3

UniProtKB/TrEMBL

A6JQY0, D3ZNR4

Conserved Domains (5) summary

cd00033
Location:698 → 752

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

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 ...

cd00063
Location:1066 → 1158

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:870 → 950

fn3; Fibronectin type III domain