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    SLAIN2 SLAIN motif family member 2 [ Homo sapiens (human) ]

    Gene ID: 57606, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SLAIN2provided by HGNC
    Official Full Name
    SLAIN motif family member 2provided by HGNC
    Primary source
    HGNC:HGNC:29282
    See related
    Ensembl:ENSG00000109171 MIM:610492; AllianceGenome:HGNC:29282
    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
    Also known as
    KIAA1458
    Summary
    Involved in cytoplasmic microtubule organization; microtubule nucleation; and positive regulation of microtubule polymerization. Located in centrosome; cytosol; and microtubule plus-end. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 22.9), esophagus (RPKM 14.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLAIN2 in Genome Data Viewer
    Location:
    4p11
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (48341529..48426201)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (48308531..48393241)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (48343546..48428218)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr4:48177274-48177775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:48187797-48188522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21547 Neighboring gene tec protein tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15405 Neighboring gene uncharacterized LOC105374445 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:48293363-48294358 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:48297678-48298877 Neighboring gene Sharpr-MPRA regulatory region 3457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21548 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:48343493-48344406 Neighboring gene U6 snRNA-associated Sm-like protein LSm2 Neighboring gene CRISPRi-validated cis-regulatory element chr4.1483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:48491403-48491940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15411 Neighboring gene solute carrier family 10 member 4 Neighboring gene zygote arrest 1 Neighboring gene FRY like transcription coactivator

    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 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. Mesenchymal Cell Invasion Requires Cooperative Regulation of Persistent Microtubule Growth by SLAIN2 and CLASP1. Bouchet BP, et al. Dev Cell, 2016 Dec 19. PMID 27939686, Free PMC Article
    2. Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene. Hirst CE, et al. Dev Biol, 2006 May 1. PMID 16546155
    3. SLAIN2 links microtubule plus end-tracking proteins and controls microtubule growth in interphase. van der Vaart B, et al. J Cell Biol, 2011 Jun 13. PMID 21646404, Free PMC Article
    4. Protein tyrosine phosphatase receptor delta acts as a neuroblastoma tumor suppressor by destabilizing the aurora kinase A oncogene. Meehan M, et al. Mol Cancer, 2012 Feb 5. PMID 22305495, Free PMC Article
    5. [IMAGE: molecular integration of the analysis of the human genome and its expression]. Auffray C, et al. C R Acad Sci III, 1995 Feb. PMID 7757816

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. catastrophe inhibition by SLAIN2 and CLASP1 supports mesenchymal cell shape in soft 3D matrices by enabling microtubules to perform a load-bearing function.
      Title: Mesenchymal Cell Invasion Requires Cooperative Regulation of Persistent Microtubule Growth by SLAIN2 and CLASP1.
    2. Results identify SLAIN2 as a key component of microtubule plus end interaction networks.
      Title: SLAIN2 links microtubule plus end-tracking proteins and controls microtubule growth in interphase.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Polymorphisms in innate immunity genes and patients response to dendritic cell-based HIV immuno-treatment.
    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
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21611

    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 cytoplasmic microtubule organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cytoplasmic microtubule organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in microtubule nucleation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in microtubule nucleation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of microtubule polymerization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of microtubule polymerization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with microtubule plus-end IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with microtubule plus-end IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SLAIN motif-containing protein 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_020846.2 → NP_065897.1  SLAIN motif-containing protein 2

      See identical proteins and their annotated locations for NP_065897.1

      Status: VALIDATED

      Source sequence(s)
      AB040891, AC096952, AC098873, BC040993, CB157681, Z25182
      Consensus CDS
      CCDS47051.1
      UniProtKB/Swiss-Prot
      A8K4P1, Q8N5R3, Q9P270
      UniProtKB/TrEMBL
      A0A024R9T6, A0A158RFV0
      Related
      ENSP00000264313.5, ENST00000264313.11
      Conserved Domains (1) summary
      pfam15301
      Location:130 → 581
      SLAIN; SLAIN motif-containing family

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      48341529..48426201
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005248121.4 → XP_005248178.1  SLAIN motif-containing protein 2 isoform X1

      Conserved Domains (1) summary
      pfam15301
      Location:130 → 607
      SLAIN; SLAIN motif-containing family

    2. XM_047416023.1 → XP_047271979.1  SLAIN motif-containing protein 2 isoform X2

      Related
      ENSP00000425923.1, ENST00000512093.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      48308531..48393241
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350613.1 → XP_054206588.1  SLAIN motif-containing protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P270.2 GenPept UniProtKB/Swiss-Prot:Q9P270

    Gene LinkOut

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

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