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    SLAIN1 SLAIN motif family member 1 [ Homo sapiens (human) ]

    Gene ID: 122060, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SLAIN1provided by HGNC
    Official Full Name
    SLAIN motif family member 1provided by HGNC
    Primary source
    HGNC:HGNC:26387
    See related
    Ensembl:ENSG00000139737 MIM:610491; AllianceGenome:HGNC:26387
    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
    C13orf32
    Summary
    Predicted to be located in cytoplasm and cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in brain (RPKM 39.3), testis (RPKM 10.8) and 7 other tissues See more
    Orthologs
    mouse all
    NEW
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    Genomic context

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    See SLAIN1 in Genome Data Viewer
    Location:
    13q22.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (77697687..77764229)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (76922360..76989219)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (78271822..78338364)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene putative UPF0607 protein ENSP00000383144 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:78237303-78237481 Neighboring gene serine palmitoyltransferase long chain base subunit 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5422 Neighboring gene microRNA 3665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7846 Neighboring gene NANOG hESC enhancer GRCh37_chr13:78358462-78359034 Neighboring gene EDNRB antisense RNA 1 Neighboring gene VISTA enhancer hs1394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:78425667-78426299 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:78427507-78428016 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:78428017-78428526 Neighboring gene EDNRB proximal promoter region Neighboring gene endothelin receptor type B Neighboring gene RNA, 7SL, cytoplasmic 810, pseudogene

    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. 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
    2. rec-YnH enables simultaneous many-by-many detection of direct protein-protein and protein-RNA interactions. Yang JS, et al. Nat Commun, 2018 Sep 14. PMID 30217970, Free PMC Article
    3. CRISPR/Cas9-mediated Genomic Editing of Cluap1/IFT38 Reveals a New Role in Actin Arrangement. Beyer T, et al. Mol Cell Proteomics, 2018 Jul. PMID 29615496, Free PMC Article
    4. A conserved acetylation switch enables pharmacological control of tubby-like protein stability. Kerek EM, et al. J Biol Chem, 2021 Jan-Jun. PMID 33187986, Free PMC Article
    5. USP45 and Spindly are part of the same complex implicated in cell migration. Conte C, et al. Sci Rep, 2018 Sep 26. PMID 30258100, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expressed at the stem cell and epiblast stages of embryonic stem cell differentiation.
      Title: Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene.
    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

    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

    • FLJ30046, MGC131899

    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 microtubule nucleation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of microtubule polymerization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    colocalizes_with microtubule plus-end IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    SLAIN motif-containing protein 1

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001040153.4 → NP_001035243.2  SLAIN motif-containing protein 1 isoform A

      See identical proteins and their annotated locations for NP_001035243.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform A.
      Source sequence(s)
      AK294201, BC045177
      Consensus CDS
      CCDS31995.2
      UniProtKB/TrEMBL
      A0A0C4DFN6
      Related
      ENSP00000418707.1, ENST00000488699.5
      Conserved Domains (1) summary
      pfam15301
      Location:46 → 426
      SLAIN; SLAIN motif-containing family

    2. NM_001242868.2 → NP_001229797.1  SLAIN motif-containing protein 1 isoform C

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 5' exon, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (C) has a distinct and longer N-terminus, compared to isoform A.
      Source sequence(s)
      AL354831, BC045177, BG391962, BQ433296, DB500463
      Consensus CDS
      CCDS73588.1
      UniProtKB/Swiss-Prot
      A8K0Z9, B7Z209, Q5T6P4, Q5T6P7, Q8ND10, Q8ND83, Q96NV0
      UniProtKB/TrEMBL
      A0A0A0MSS3
      Related
      ENSP00000400921.2, ENST00000418532.6
      Conserved Domains (1) summary
      pfam15301
      Location:209 → 590
      SLAIN; SLAIN motif-containing family

    3. NM_001242869.2 → NP_001229798.1  SLAIN motif-containing protein 1 isoform D

      See identical proteins and their annotated locations for NP_001229798.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon, and lacks an internal in-frame coding exon, compared to variant 1. The encoded isoform (D) is shorter at the N-terminus and lacks an internal segment, compared to isoform A. Both variants 4 and 5 encode isoform D.
      Source sequence(s)
      AK289600, DA096260, DA343547
      Consensus CDS
      CCDS55901.1
      UniProtKB/Swiss-Prot
      Q8ND83
      Related
      ENSP00000314443.5, ENST00000314070.9
      Conserved Domains (1) summary
      pfam15301
      Location:20 → 191
      SLAIN; SLAIN motif-containing family

    4. NM_001242870.2 → NP_001229799.1  SLAIN motif-containing protein 1 isoform D

      See identical proteins and their annotated locations for NP_001229799.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon, and lacks an internal in-frame coding exon, compared to variant 1. The encoded isoform (D) is shorter at the N-terminus and lacks an internal segment, compared to isoform A. Both variants 4 and 5 encode isoform D.
      Source sequence(s)
      AL834203, DA343547
      Consensus CDS
      CCDS55901.1
      UniProtKB/Swiss-Prot
      Q8ND83
      Conserved Domains (1) summary
      pfam15301
      Location:20 → 191
      SLAIN; SLAIN motif-containing family

    5. NM_001242871.2 → NP_001229800.1  SLAIN motif-containing protein 1 isoform E

      See identical proteins and their annotated locations for NP_001229800.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, uses an alternate start codon, and includes an alternate splice site in its 5' coding region, compared to variant 1. The encoded isoform (E) has a distinct and shorter N-terminus, compared to isoform A.
      Source sequence(s)
      AK295423, BC045177, DA343547
      Consensus CDS
      CCDS73589.1
      UniProtKB/TrEMBL
      A0A0C4DFN6, B7Z326
      Related
      ENSP00000314546.8, ENST00000351546.7
      Conserved Domains (1) summary
      pfam15301
      Location:21 → 304
      SLAIN; SLAIN motif-containing family

    6. NM_001366665.1 → NP_001353594.1  SLAIN motif-containing protein 1 isoform F

      Status: VALIDATED

      Source sequence(s)
      AL354831
      Consensus CDS
      CCDS91821.1
      UniProtKB/TrEMBL
      A0A994J5K0
      Related
      ENSP00000516138.1, ENST00000705543.1
      Conserved Domains (1) summary
      pfam15301
      Location:46 → 476
      SLAIN; SLAIN motif-containing family

    7. NM_001366666.1 → NP_001353595.1  SLAIN motif-containing protein 1 isoform B

      Status: VALIDATED

      Source sequence(s)
      AL354831
      Consensus CDS
      CCDS9460.1
      UniProtKB/TrEMBL
      A0A0C4DFN6
      Related
      ENSP00000351507.2, ENST00000358679.3
      Conserved Domains (1) summary
      pfam15301
      Location:1 → 305
      SLAIN; SLAIN motif-containing family

    8. NM_001411026.1 → NP_001397955.1  SLAIN motif-containing protein 1 isoform G

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) represents the allele encoded by the GRCh38 reference genome and encodes isoform (G).
      Source sequence(s)
      AL354831
      Consensus CDS
      CCDS91820.1
      UniProtKB/TrEMBL
      Q5T6P1
      Related
      ENSP00000403049.2, ENST00000446759.6

    9. NM_001412123.1 → NP_001399052.1  SLAIN motif-containing protein 1 isoform H

      Status: VALIDATED

      Source sequence(s)
      CP068265

    10. NM_001412125.1 → NP_001399054.1  SLAIN motif-containing protein 1 isoform I

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11) uses the same exon combination as variant 9 but represents the allele encoded by the T2T genome assembly. The encoded isoform (I) has a slightly different sequence in the N-terminal region compared to isoform G.
      Source sequence(s)
      CP068265

    11. NM_144595.4 → NP_653196.1  SLAIN motif-containing protein 1 isoform B

      See identical proteins and their annotated locations for NP_653196.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (B) is shorter at the N-terminus, compared to isoform A.
      Source sequence(s)
      BC045177, DA343547
      Consensus CDS
      CCDS9460.1
      UniProtKB/TrEMBL
      A0A0C4DFN6
      Conserved Domains (1) summary
      pfam15301
      Location:1 → 305
      SLAIN; SLAIN motif-containing family

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      77697687..77764229
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      76922360..76989219
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8ND83.3 GenPept UniProtKB/Swiss-Prot:Q8ND83

    Gene LinkOut

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

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