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SDK2 sidekick cell adhesion molecule 2 [ Homo sapiens (human) ]

Gene ID: 54549, updated on 5-Mar-2024

Summary

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Official Symbol
SDK2provided by HGNC
Official Full Name
sidekick cell adhesion molecule 2provided by HGNC
Primary source
HGNC:HGNC:19308
See related
Ensembl:ENSG00000069188 MIM:607217; AllianceGenome:HGNC:19308
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
Summary
The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains two immunoglobulin 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. This protein, and a homologous mouse sequence, are very similar to the Drosophila sidekick gene product but the specific function of this superfamily member is not yet known. Evidence for alternative splicing at this gene locus has been observed but the full-length nature of additional variants has not yet been determined. [provided by RefSeq, Jul 2008]
Expression
Biased expression in testis (RPKM 6.4), spleen (RPKM 1.7) and 8 other tissues See more
Orthologs
mouse all
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Genomic context

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See SDK2 in Genome Data Viewer
Location:
17q25.1
Exon count:
47
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (73334384..73644445, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (74224177..74535383, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (71330523..71640584, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12693 Neighboring gene mitochondrial nucleoid associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71280886-71281442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71281998-71282553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71282554-71283108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12695 Neighboring gene cleavage and polyadenylation specific factor 4 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71287907-71288788 Neighboring gene Sharpr-MPRA regulatory region 4436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8925 Neighboring gene CDC42 effector protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71314086-71314838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71332871-71333770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71343461-71344310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71348097-71348598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71348599-71349098 Neighboring gene Sharpr-MPRA regulatory region 1327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71357197-71357868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71359686-71360661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71361126-71361628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71375179-71375680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71376229-71376730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71376731-71377230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71396825-71397329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71397330-71397833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71434193-71434693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12699 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71487500-71488358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71488359-71489217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71501870-71502807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71503745-71504682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71507033-71507902 Neighboring gene uncharacterized LOC101928251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71530725-71531437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71533005-71533777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71536899-71537463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71542356-71542892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71544460-71544960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71544961-71545461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71556405-71557010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71557011-71557617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71560304-71560804 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:71561780-71562370 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:71562371-71562960 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71563551-71564139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71584531-71585034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71585035-71585539 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:71585540-71586043 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:71586044-71586548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71591289-71591834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71608178-71608714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71621555-71622080 Neighboring gene uncharacterized LOC124904054 Neighboring gene NANOG hESC enhancer GRCh37_chr17:71649316-71649844 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:71682138-71682716 Neighboring gene NANOG hESC enhancer GRCh37_chr17:71731954-71732466 Neighboring gene uncharacterized LOC100134391 Neighboring gene long intergenic non-protein coding RNA 469

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. Sidekick-1 is upregulated in glomeruli in HIV-associated nephropathy. Kaufman L, et al. J Am Soc Nephrol, 2004 Jul. PMID 15213259
  2. Sidekicks: synaptic adhesion molecules that promote lamina-specific connectivity in the retina. Yamagata M, et al. Cell, 2002 Sep 6. PMID 12230981
  3. The sidekick gene, a member of the immunoglobulin superfamily, is required for pattern formation in the Drosophila eye. Nguyen DN, et al. Development, 1997 Sep. PMID 9310325
  4. Genome-wide association study of panic disorder in the Japanese population. Otowa T, et al. J Hum Genet, 2009 Feb. PMID 19165232
  5. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Zody MC, et al. Nature, 2006 Apr 20. PMID 16625196, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genome-wide association study of panic disorder in the Japanese population.
Submit: New GeneRIF Correction

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 panic disorder in the Japanese population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10832, KIAA1514

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in camera-type eye photoreceptor cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in retina layer formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in plasma membrane TAS
Traceable Author Statement
more info
  
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
protein sidekick-2
Names
sidekick homolog 2

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_001144952.2 → NP_001138424.1  protein sidekick-2 precursor

    See identical proteins and their annotated locations for NP_001138424.1

    Status: VALIDATED

    Source sequence(s)
    AB040947, AC032019, AC087301, AC124804, BC066363
    Consensus CDS
    CCDS45769.1
    UniProtKB/Swiss-Prot
    A6NMR8, C9JA57, Q58EX2, Q86VY3, Q9NTD2, Q9NVB3, Q9P214
    Related
    ENSP00000376421.3, ENST00000392650.8
    Conserved Domains (6) summary
    cd00096
    Location:326 → 394
    Ig; Immunoglobulin domain
    smart00408
    Location:233 → 286
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:502 → 586
    IG_like; Immunoglobulin like
    cd00063
    Location:1626 → 1719
    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:402 → 492
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:416 → 492
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    73334384..73644445 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047436313.1 → XP_047292269.1  protein sidekick-2 isoform X3

  2. XM_011524914.3 → XP_011523216.1  protein sidekick-2 isoform X1

    UniProtKB/Swiss-Prot
    Q58EX2
    Conserved Domains (6) summary
    cd00096
    Location:326 → 394
    Ig; Immunoglobulin domain
    smart00408
    Location:233 → 286
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:502 → 586
    IG_like; Immunoglobulin like
    cd00063
    Location:1607 → 1700
    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:402 → 492
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:416 → 492
    Ig; Immunoglobulin domain

  3. XM_011524915.3 → XP_011523217.1  protein sidekick-2 isoform X2

    Conserved Domains (6) summary
    cd00096
    Location:326 → 394
    Ig; Immunoglobulin domain
    smart00408
    Location:233 → 286
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:502 → 586
    IG_like; Immunoglobulin like
    cd00063
    Location:1626 → 1719
    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:402 → 492
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:416 → 492
    Ig; Immunoglobulin domain

  4. XM_011524916.4 → XP_011523218.1  protein sidekick-2 isoform X4

    Conserved Domains (6) summary
    cd00096
    Location:326 → 394
    Ig; Immunoglobulin domain
    smart00408
    Location:233 → 286
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:502 → 586
    IG_like; Immunoglobulin like
    cd00063
    Location:590 → 681
    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:402 → 492
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:416 → 492
    Ig; Immunoglobulin domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    74224177..74535383 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316536.1 → XP_054172511.1  protein sidekick-2 isoform X3

  2. XM_054316534.1 → XP_054172509.1  protein sidekick-2 isoform X1

  3. XM_054316535.1 → XP_054172510.1  protein sidekick-2 isoform X2

  4. XM_054316537.1 → XP_054172512.1  protein sidekick-2 isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_019064.3: Suppressed sequence

    Description
    NM_019064.3: This RefSeq was temporarily suppressed because the CDS was partial.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q58EX2.3 GenPept UniProtKB/Swiss-Prot:Q58EX2

Gene LinkOut

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