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

    Gene ID: 221935, updated on 3-Dec-2024

    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    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

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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, Q8TEN9, Q8TEP5, Q96N44
      UniProtKB/TrEMBL
      F8W6X9
      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: 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_047420038.1XP_047275994.1  protein sidekick-1 isoform X4

      UniProtKB/TrEMBL
      F8W6X9
    2. XM_047420037.1XP_047275993.1  protein sidekick-1 isoform X3

      UniProtKB/TrEMBL
      F8W6X9
    3. XM_024446683.2XP_024302451.1  protein sidekick-1 isoform X1

      UniProtKB/TrEMBL
      F8W6X9
      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
    4. XM_024446684.2XP_024302452.1  protein sidekick-1 isoform X2

      UniProtKB/TrEMBL
      F8W6X9
      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

    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_054357556.1XP_054213531.1  protein sidekick-1 isoform X3

      UniProtKB/TrEMBL
      F8W6X9
    2. XM_054357557.1XP_054213532.1  protein sidekick-1 isoform X4

      UniProtKB/TrEMBL
      F8W6X9
    3. XM_054357554.1XP_054213529.1  protein sidekick-1 isoform X1

      UniProtKB/TrEMBL
      F8W6X9
    4. XM_054357555.1XP_054213530.1  protein sidekick-1 isoform X2

      UniProtKB/TrEMBL
      F8W6X9