Sdk1 sidekick cell adhesion molecule 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sdk1provided by RGD
Official Full Name: sidekick cell adhesion molecule 1provided by RGD
Primary source: RGD:1560686
See related: Ensembl:ENSRNOG00000001103 AllianceGenome:RGD:1560686
Gene type: protein coding
RefSeq status: MODEL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1560686
Summary: Predicted to act upstream of or within behavioral response to cocaine and regulation of dendritic spine development. Orthologous to human SDK1 (sidekick cell adhesion molecule 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 108.4), Kidney (RPKM 27.3) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 12q11

Exon count:: 47

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (17491430..18477914, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (12378074..13363934, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (14445798..15443442, complement)

Chromosome 12 - NC_086030.1 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?

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General gene information

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Markers

d12rat39 (e-PCR)
- UniSTS:120833

d12rat4 (e-PCR)
- UniSTS:120834

D12Got26 (e-PCR)
- UniSTS:111881

AU029165 (e-PCR)
- UniSTS:111639

D12Wox13 (e-PCR)
- UniSTS:518688

D12Hmgc3 (e-PCR)
- UniSTS:545878

44.MMHAP70FRG11.seq (e-PCR)
- UniSTS:124547

D12Arb8 (e-PCR), detects polymorphism
- UniSTS:226441

BE117712 (e-PCR)
- UniSTS:248714

RH45568 (e-PCR)
- UniSTS:58258

RH139306 (e-PCR)
- UniSTS:221392

BF405084 (e-PCR)
- UniSTS:247777

BF396334 (e-PCR)
- UniSTS:245750

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
acts_upstream_of_or_within behavioral response to cocaine	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of dendritic spine development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein sidekick-1

NCBI Reference Sequences (RefSeq)

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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_086030.1 Reference GRCr8

Range

17491430..18477914 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063271861.1 → XP_063127931.1 protein sidekick-1 isoform X2
XM_039089863.2 → XP_038945791.1 protein sidekick-1 isoform X1

UniProtKB/TrEMBL

A0A8I6A427

Related

ENSRNOP00000086581.1

Conserved Domains (7) summary

PHA03307
Location:38 → 162

PHA03307; transcriptional regulator ICP4; Provisional

cd00063
Location:1799 → 1892

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:765 → 850

fn3; Fibronectin type III domain

pfam07679
Location:575 → 665

I-set; Immunoglobulin I-set domain

pfam13927
Location:388 → 460

Ig_3; Immunoglobulin domain

cd00096
Location:583 → 586

Ig; Ig strand A' [structural motif]

cl11960
Location:481 → 570

Ig; Immunoglobulin domain
XM_039089864.2 → XP_038945792.1 protein sidekick-1 isoform X3

Conserved Domains (6) summary

cd00063
Location:1414 → 1507

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:380 → 465

fn3; Fibronectin type III domain

pfam07679
Location:190 → 280

I-set; Immunoglobulin I-set domain

pfam13927
Location:3 → 75

Ig_3; Immunoglobulin domain

cd00096
Location:198 → 201

Ig; Ig strand A' [structural motif]

cl11960
Location:96 → 185

Ig; Immunoglobulin domain
XM_063271862.1 → XP_063127932.1 protein sidekick-1 isoform X3