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

    Gene ID: 221935, updated on 10-Dec-2024

    Summary

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    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; AllianceGenome:HGNC:19307
    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
    mouse all
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    Genomic context

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    See SDK1 in Genome Data Viewer
    Location:
    7p22.2
    Exon count:
    46
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (3301252..4269000)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (3415529..4385763)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (3340884..4308632)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:3234434-3235114 Neighboring gene uncharacterized LOC124901574 Neighboring gene uncharacterized LOC124901575 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:3283525-3284724 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:3320540-3321077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:3339451-3339963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:3339964-3340475 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:3341185-3341685 Neighboring gene SDK1 antisense RNA 1 Neighboring gene uncharacterized LOC124901577 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:3439188-3439937 Neighboring gene ribosomal protein L21 pseudogene 72 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:3492607-3493001 Neighboring gene NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:3723703-3724203 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:3752169-3752670 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:3752671-3753170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:3761680-3762223 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:3762224-3762766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:3827296-3827796 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:3950537-3951736 Neighboring gene uncharacterized LOC124901576 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:4007911-4009110 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:4079787-4080423 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:4080424-4081059 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4082400-4082925 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:4118749-4118965 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4128978-4129522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4142403-4142903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4145852-4146434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4147017-4147598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4148767-4149268 Neighboring gene uncharacterized LOC105375131 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4175261-4176143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4176144-4177025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4186737-4187351 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4208580-4209080 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:4214126-4214549 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4220886-4221386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4221387-4221887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4226243-4226988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4229670-4230550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4234799-4235418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4237901-4238400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4242006-4242522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4242523-4243039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4245119-4245620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4245621-4246120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:4256703-4257426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4265444-4265945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4265946-4266446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:4276819-4277320 Neighboring gene NANOG hESC enhancer GRCh37_chr7:4279685-4280186 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:4299431-4300630 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:4303312-4304511 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:4347010-4347752 Neighboring gene uncharacterized LOC124901578 Neighboring gene uncharacterized LOC124901579

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Novel loci for ocular axial length identified through extreme-phenotype genome-wide association study in Chinese populations. Han X, et al. Br J Ophthalmol, 2024 May 21. PMID 37524447
    2. The homophilic adhesion molecule sidekick-1 contributes to augmented podocyte aggregation in HIV-associated nephropathy. Kaufman L, et al. FASEB J, 2007 May. PMID 17307840
    3. A genome-wide association study for malignant mesothelioma risk. Cadby G, et al. Lung Cancer, 2013 Oct. PMID 23827383
    4. Sidekicks: synaptic adhesion molecules that promote lamina-specific connectivity in the retina. Yamagata M, et al. Cell, 2002 Sep 6. PMID 12230981
    5. Up-regulation of the homophilic adhesion molecule sidekick-1 in podocytes contributes to glomerulosclerosis. Kaufman L, et al. J Biol Chem, 2010 Aug 13. PMID 20562105, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel loci for ocular axial length identified through extreme-phenotype genome-wide association study in Chinese populations.
      Title: Novel loci for ocular axial length identified through extreme-phenotype genome-wide association study in Chinese populations.
    2. SDK1 could possibly serve as a candidate gene for alterations associated with asbestos exposure.
      Title: Driver Gene and Novel Mutations in Asbestos-Exposed Lung Adenocarcinoma and Malignant Mesothelioma Detected by Exome Sequencing.
    3. Case-control studies reveal malignant mesothelioma risk associated with variants in the SDK1, CRTAM and RASGRF2 genes.
      Title: A genome-wide association study for malignant mesothelioma risk.
    4. Data conclude that the up-regulation of sdk-1 in podocytes is an important pathogenic factor in glomerulosclerosis and that the mechanism involves disruption of the actin cytoskeleton possibly via alterations in MAGI-1 function.
      Title: Up-regulation of the homophilic adhesion molecule sidekick-1 in podocytes contributes to glomerulosclerosis.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. SDK1 may be a susceptibility gene for hypertension in Japanese individuals, although the functional relevance of the identified polymorphism was not determined.
      Title: Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients.
    8. dysregulation of sdk-1 protein may play an important role in HIV-associated nephropathy pathogenesis
      Title: Sidekick-1 is upregulated in glomeruli in HIV-associated nephropathy.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

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

    • FLJ31425

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in behavioral response to cocaine IEA
    Inferred from Electronic Annotation
    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 regulation of dendritic spine development IEA
    Inferred from Electronic Annotation
    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-1
    Names
    sidekick homolog 1, cell adhesion molecule

    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.

    Genomic

    1. NG_051298.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001079653.2 → NP_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:191 → 284
      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_152744.4 → NP_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, Q8TEN9, Q8TEP5, Q96N44
      UniProtKB/TrEMBL
      F8W6X9
      Related
      ENSP00000385899.2, ENST00000404826.7
      Conserved Domains (6) summary
      cd00096
      Location:404 → 472
      Ig; Immunoglobulin domain
      smart00408
      Location:312 → 364
      IGc2; Immunoglobulin C-2 Type
      cd00063
      Location:1704 → 1797
      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:480 → 570
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:771 → 857
      fn3; Fibronectin type III domain
      cl11960
      Location:494 → 570
      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_000007.14 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047420038.1 → XP_047275994.1  protein sidekick-1 isoform X4

      UniProtKB/TrEMBL
      F8W6X9

    2. XM_047420037.1 → XP_047275993.1  protein sidekick-1 isoform X3

      UniProtKB/TrEMBL
      F8W6X9

    3. XM_024446683.2 → XP_024302451.1  protein sidekick-1 isoform X1

      UniProtKB/TrEMBL
      F8W6X9
      Conserved Domains (6) summary
      cd00063
      Location:1453 → 1546
      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:229 → 319
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:722 → 803
      fn3; Fibronectin type III domain
      pfam13927
      Location:42 → 113
      Ig_3; Immunoglobulin domain
      cl11960
      Location:329 → 413
      Ig; Immunoglobulin domain
      cl28434
      Location:135 → 224
      I-set; Immunoglobulin I-set domain

    4. XM_024446684.2 → XP_024302452.1  protein sidekick-1 isoform X2

      UniProtKB/TrEMBL
      F8W6X9
      Conserved Domains (6) summary
      cd00063
      Location:1433 → 1526
      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:229 → 319
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:722 → 803
      fn3; Fibronectin type III domain
      pfam13927
      Location:42 → 113
      Ig_3; Immunoglobulin domain
      cl11960
      Location:329 → 413
      Ig; Immunoglobulin domain
      cl28434
      Location:135 → 224
      I-set; Immunoglobulin I-set domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      3415529..4385763
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357556.1 → XP_054213531.1  protein sidekick-1 isoform X3

      UniProtKB/TrEMBL
      F8W6X9

    2. XM_054357557.1 → XP_054213532.1  protein sidekick-1 isoform X4

      UniProtKB/TrEMBL
      F8W6X9

    3. XM_054357554.1 → XP_054213529.1  protein sidekick-1 isoform X1

      UniProtKB/TrEMBL
      F8W6X9

    4. XM_054357555.1 → XP_054213530.1  protein sidekick-1 isoform X2

      UniProtKB/TrEMBL
      F8W6X9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z5N4.3 GenPept UniProtKB/Swiss-Prot:Q7Z5N4

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