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SDK1 sidekick cell adhesion molecule 1 [ Homo sapiens (human) ]

Gene ID: 221935, updated on 29-Mar-2020

Summary

Official Symbol
SDK1provided by HGNC
Official Full Name
sidekick cell adhesion molecule 1provided by HGNC
Primary source
HGNC:HGNC:19307
See related
Ensembl:ENSG00000146555 MIM:607216
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains six immunoglobulin-like domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
Expression
Broad expression in endometrium (RPKM 2.3), spleen (RPKM 2.1) and 22 other tissues See more
Orthologs

Genomic context

See SDK1 in Genome Data Viewer
Location:
7p22.2
Exon count:
49
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (3301252..4269000)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (3341080..4308632)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375130 Neighboring gene uncharacterized LOC100129603 Neighboring gene SDK1 antisense RNA 1 Neighboring gene ribosomal protein L21 pseudogene 72 Neighboring gene NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae) Neighboring gene uncharacterized LOC105375131 Neighboring gene uncharacterized LOC105375133 Neighboring gene cytochrome P450 family 3 subfamily A member 54, pseudogene

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ31425

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
behavioral response to cocaine IEA
Inferred from Electronic Annotation
more info
 
cell-cell junction organization TAS
Traceable Author Statement
more info
 
homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of dendritic spine development IEA
Inferred from Electronic Annotation
more info
 
retina layer formation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retina layer formation ISS
Inferred from Sequence or Structural Similarity
more info
 
synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
protein sidekick-1
Names
sidekick homolog 1, cell adhesion molecule

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_051298.1 RefSeqGene

    Range
    4805..972553
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001079653.2NP_001073121.1  protein sidekick-1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks several exons in the 5' coding region, uses a downstream in-frame start codon, and differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a significantly shorter N-terminus and a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL833354, DB065853, DB454012
    Related
    ENST00000476701.5
    Conserved Domains (1) summary
    cd00063
    Location:191284
    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 ...
  2. NM_152744.4NP_689957.3  protein sidekick-1 isoform 1

    See identical proteins and their annotated locations for NP_689957.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC015968, AC017000, AC073316, AL833354, AY310398, DB065853
    Consensus CDS
    CCDS34590.1
    UniProtKB/Swiss-Prot
    Q7Z5N4
    Related
    ENSP00000385899.2, ENST00000404826.7
    Conserved Domains (6) summary
    cd00096
    Location:404472
    Ig; Immunoglobulin domain
    smart00408
    Location:312364
    IGc2; Immunoglobulin C-2 Type
    cd00063
    Location:17041797
    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 ...
    pfam07679
    Location:480570
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:771857
    fn3; Fibronectin type III domain
    cl11960
    Location:494570
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    3301252..4269000
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446683.1XP_024302451.1  protein sidekick-1 isoform X2

    Conserved Domains (6) summary
    cd00063
    Location:14531546
    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 ...
    pfam07679
    Location:229319
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:722803
    fn3; Fibronectin type III domain
    pfam13927
    Location:42113
    Ig_3; Immunoglobulin domain
    cl11960
    Location:329413
    Ig; Immunoglobulin domain
    cl28434
    Location:135224
    I-set; Immunoglobulin I-set domain
  2. XM_024446684.1XP_024302452.1  protein sidekick-1 isoform X3

    Conserved Domains (6) summary
    cd00063
    Location:14331526
    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 ...
    pfam07679
    Location:229319
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:722803
    fn3; Fibronectin type III domain
    pfam13927
    Location:42113
    Ig_3; Immunoglobulin domain
    cl11960
    Location:329413
    Ig; Immunoglobulin domain
    cl28434
    Location:135224
    I-set; Immunoglobulin I-set domain
  3. XM_017011837.1XP_016867326.1  protein sidekick-1 isoform X1

  4. XM_011515188.1XP_011513490.1  protein sidekick-1 isoform X4

    Conserved Domains (4) summary
    cd00063
    Location:12951388
    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 ...
    pfam07679
    Location:70160
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:361447
    fn3; Fibronectin type III domain
    cl11960
    Location:84160
    Ig; Immunoglobulin domain
  5. XM_011515189.1XP_011513491.1  protein sidekick-1 isoform X5

    Conserved Domains (4) summary
    cd00063
    Location:12941387
    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 ...
    pfam07679
    Location:70160
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:361447
    fn3; Fibronectin type III domain
    cl11960
    Location:84160
    Ig; Immunoglobulin domain
  6. XM_011515190.1XP_011513492.1  protein sidekick-1 isoform X6

    Conserved Domains (4) summary
    cd00063
    Location:12951388
    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 ...
    pfam07679
    Location:70160
    I-set; Immunoglobulin I-set domain
    pfam00041
    Location:361447
    fn3; Fibronectin type III domain
    cl11960
    Location:84160
    Ig; Immunoglobulin domain
  7. XM_017011838.1XP_016867327.1  protein sidekick-1 isoform X7

  8. XM_017011839.1XP_016867328.1  protein sidekick-1 isoform X8

  9. XM_017011840.1XP_016867329.1  protein sidekick-1 isoform X9

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