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    STMN3 stathmin 3 [ Homo sapiens (human) ]

    Gene ID: 50861, updated on 9-Dec-2024

    Summary

    Official Symbol
    STMN3provided by HGNC
    Official Full Name
    stathmin 3provided by HGNC
    Primary source
    HGNC:HGNC:15926
    See related
    Ensembl:ENSG00000197457 MIM:608362; AllianceGenome:HGNC:15926
    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
    Also known as
    SCLIP
    Summary
    This gene encodes a protein which is a member of the stathmin protein family. Members of this protein family form a complex with tubulins at a ratio of 2 tubulins for each stathmin protein. Microtubules require the ordered assembly of alpha- and beta-tubulins, and formation of a complex with stathmin disrupts microtubule formation and function. A pseudogene of this gene is located on chromosome 22. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
    Expression
    Broad expression in brain (RPKM 62.0), thyroid (RPKM 16.1) and 20 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See STMN3 in Genome Data Viewer
    Location:
    20q13.33
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63639712..63653424, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65453599..65467540, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62271065..62284777, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61137 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61148 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61158 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61169 Neighboring gene glucocorticoid modulatory element binding protein 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61181 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61184 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18235 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62250681-62251180 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13168 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18236 Neighboring gene melanoma highly expressed competing endogenous lncRNA for miR-425 and miR-489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62269990-62270750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62272271-62273029 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62273358-62274096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62275446-62276015 Neighboring gene Sharpr-MPRA regulatory region 12780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62282910-62283480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62284757-62285436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62285437-62286115 Neighboring gene RTEL1-TNFRSF6B readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18241 Neighboring gene regulator of telomere elongation helicase 1 Neighboring gene uncharacterized LOC124904954 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62307938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62313341-62314065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62314792-62315516 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62320674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18243 Neighboring gene TNF receptor superfamily member 6b Neighboring gene ARF related protein 1

    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
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables tubulin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in blastocyst hatching IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cytoplasmic microtubule organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in microtubule depolymerization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of Rac protein signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neuron projection development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of microtubule polymerization or depolymerization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in growth cone IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in neuron projection IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    stathmin-3
    Names
    SCG10-like protein
    stathmin-like 3

    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.

    mRNA and Protein(s)

    1. NM_001276310.2NP_001263239.1  stathmin-3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001263239.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' exon and uses a downstream start codon, compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK298903, AL353715
      Consensus CDS
      CCDS63330.1
      UniProtKB/TrEMBL
      Q8NCA8
      Related
      ENSP00000439840.1, ENST00000540534.5
      Conserved Domains (1) summary
      pfam00836
      Location:28164
      Stathmin; Stathmin family
    2. NM_015894.4NP_056978.2  stathmin-3 isoform 1

      See identical proteins and their annotated locations for NP_056978.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
      Source sequence(s)
      AK131326, BC009381, BC056873, BX449528, DB564475
      Consensus CDS
      CCDS13529.1
      UniProtKB/Swiss-Prot
      B3KSQ5, B7WP52, B7Z5G4, O75527, Q969Y4, Q9NZ72
      UniProtKB/TrEMBL
      Q8NCA8
      Related
      ENSP00000359070.1, ENST00000370053.3
      Conserved Domains (1) summary
      pfam00836
      Location:39175
      Stathmin; Stathmin family

    RNA

    1. NR_075070.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK310010, AL353715

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      63639712..63653424 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      65453599..65467540 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)