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

    Gene ID: 54549, updated on 10-Dec-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (73334384..73644445, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (74224177..74535383, complement)
    RS_2024_09 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. Sidekicks: synaptic adhesion molecules that promote lamina-specific connectivity in the retina. Yamagata M, et al. Cell, 2002 Sep 6. PMID 12230981
    2. Sidekick-1 is upregulated in glomeruli in HIV-associated nephropathy. Kaufman L, et al. J Am Soc Nephrol, 2004 Jul. PMID 15213259
    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 (24) 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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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