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STMN3 stathmin 3 [ Homo sapiens (human) ]

Gene ID: 50861, updated on 17-Sep-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
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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 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 GTPase activity 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)

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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_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)