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SHTN1 shootin 1 [ Homo sapiens (human) ]

Gene ID: 57698, updated on 5-Mar-2024

Summary

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Official Symbol
SHTN1provided by HGNC
Official Full Name
shootin 1provided by HGNC
Primary source
HGNC:HGNC:29319
See related
Ensembl:ENSG00000187164 MIM:611171; AllianceGenome:HGNC:29319
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
KIAA1598; shootin-1
Summary
Enables identical protein binding activity. Involved in positive regulation of neuron migration. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 8.9), thyroid (RPKM 3.4) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
10q25.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (116881477..117126586, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (117775790..118020853, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (118640988..118886097, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene heat shock protein family A (Hsp70) member 12A Neighboring gene uncharacterized LOC105378498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:118534387-118534886 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:118538206-118539405 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:118544309-118544475 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:118595447-118596082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4095 Neighboring gene microRNA 9851 Neighboring gene enolase 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:118665638-118666837 Neighboring gene Sharpr-MPRA regulatory region 1976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2857 Neighboring gene VISTA enhancer hs841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:118885664-118886164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:118890627-118891154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:118891155-118891681 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:118899364-118899950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:118899951-118900536 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:118918871-118919627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:118925104-118925658 Neighboring gene MIR3663 host gene Neighboring gene ventral anterior homeobox 1 Neighboring gene microRNA 3663

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. Putative Coiled-Coil Domain-Dependent Autoinhibition and Alternative Splicing Determine SHTN1's Actin-Binding Activity. Ergin V, et al. J Mol Biol, 2020 Jun 26. PMID 32371045, Free PMC Article
  2. Rnaset2 inhibits melanocyte outgrowth possibly through interacting with shootin1. Wang Q, et al. J Dermatol Sci, 2015 Oct. PMID 26293343
  3. Associations of genetic variants in endocytic trafficking of epidermal growth factor receptor super pathway with risk of nonsyndromic cleft lip with or without cleft palate. Li B, et al. Mol Genet Genomic Med, 2018 Nov. PMID 30411541, Free PMC Article
  4. Shootin1 interacts with actin retrograde flow and L1-CAM to promote axon outgrowth. Shimada T, et al. J Cell Biol, 2008 Jun 2. PMID 18519736, Free PMC Article
  5. Shootin1: A protein involved in the organization of an asymmetric signal for neuronal polarization. Toriyama M, et al. J Cell Biol, 2006 Oct 9. PMID 17030985, Free PMC Article

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Putative Coiled-Coil Domain-Dependent Autoinhibition and Alternative Splicing Determine SHTN1's Actin-Binding Activity.
    Title: Putative Coiled-Coil Domain-Dependent Autoinhibition and Alternative Splicing Determine SHTN1's Actin-Binding Activity.
  2. SHTN1 might be associated with the development of nonsyndromic cleft lip with or without cleft palate.
    Title: Associations of genetic variants in endocytic trafficking of epidermal growth factor receptor super pathway with risk of nonsyndromic cleft lip with or without cleft palate.
  3. Rnaset2 inhibits melanocyte outgrowth through interacting with shootin1, and this effect may be associated with vitiligo pathogenesis.
    Title: Rnaset2 inhibits melanocyte outgrowth possibly through interacting with shootin1.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate.
EBI GWAS Catalog
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1598, MGC40476, DKFZp686A0439

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin filament binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables cadherin binding HDA PubMed 
enables kinesin binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Cdc42 protein signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in Ras protein signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in actin filament bundle retrograde transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in axonogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cytoplasmic actin-based contraction involved in cell motility ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in endoplasmic reticulum polarization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in netrin-activated signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in neuron projection morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron projection morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of axon extension ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of neuron migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of neuron migration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of establishment of cell polarity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in substrate-dependent cell migration, cell extension ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in axon ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in axonal growth cone IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in axonal growth cone ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cell leading edge IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cell leading edge ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in filopodium ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in growth cone ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in lamellipodium ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in microtubule IEA
Inferred from Electronic Annotation
more info
  
part_of microtubule associated complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in microtubule cytoskeleton ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in perikaryon ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
shootin-1
Names
shootin1

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_001127211.3 → NP_001120683.1  shootin-1 isoform a

    See identical proteins and their annotated locations for NP_001120683.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a, also known as shootin 1b).
    Source sequence(s)
    AC023283, BC022348, BC032303, BE348500, BE897523, BI086871, DN993119
    Consensus CDS
    CCDS44482.1
    UniProtKB/Swiss-Prot
    A0MZ66, A8MYU7, B3KRD3, B3KRH2, B3KTE0, B3KTJ7, B3KTJ8, B4E3U1, B7Z7Z9, Q68DG1, Q6PIM5, Q9HCH4, Q9NUV0
    Related
    ENSP00000347532.4, ENST00000355371.9
    Conserved Domains (2) summary
    pfam06156
    Location:141 → 189
    DUF972; Protein of unknown function (DUF972)
    pfam10267
    Location:268 → 350
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein

  2. NM_001258298.2 → NP_001245227.1  shootin-1 isoform c

    See identical proteins and their annotated locations for NP_001245227.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' coding region compared to variant 1, which results in translation initiation from an in-frame downstream AUG, and an isoform (c) with a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AC023283, AK304865, BC022348, BE348500, BE897523, BI086871
    Consensus CDS
    CCDS73207.1
    UniProtKB/Swiss-Prot
    A0MZ66
    Related
    ENSP00000260777.11, ENST00000260777.14
    Conserved Domains (2) summary
    pfam06156
    Location:81 → 129
    DUF972; Protein of unknown function (DUF972)
    pfam10267
    Location:208 → 290
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein

  3. NM_001258299.2 → NP_001245228.1  shootin-1 isoform d

    See identical proteins and their annotated locations for NP_001245228.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate 3' terminal exon compared to variant 1, which results in a shorter isoform (d) with a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AK302705, BC032303, DN993119
    Consensus CDS
    CCDS73208.1
    UniProtKB/Swiss-Prot
    A0MZ66
    Related
    ENSP00000376636.3, ENST00000392903.3
    Conserved Domains (1) summary
    cl25732
    Location:140 → 350
    SMC_N; RecF/RecN/SMC N terminal domain

  4. NM_001258300.1 → NP_001245229.1  shootin-1 isoform e

    See identical proteins and their annotated locations for NP_001245229.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs at the 5' and 3' ends compared to variant 1, which results in translation initiation from an in-frame downstream AUG, and an isoform (d) with a shorter N-terminus and a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AK302705, DC402821
    Consensus CDS
    CCDS58097.1
    UniProtKB/Swiss-Prot
    A0MZ66
    Related
    ENSP00000376635.4, ENST00000392901.10
    Conserved Domains (1) summary
    cl25732
    Location:80 → 290
    SMC_N; RecF/RecN/SMC N terminal domain

  5. NM_018330.7 → NP_060800.2  shootin-1 isoform b

    See identical proteins and their annotated locations for NP_060800.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two consecutive exons in the 3' coding region compared to variant 1, which results in a frame-shift and a shorter isoform (b, also known as shootin 1a) with a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC023283, AK095703, BC022348, BE348500, BE897523, BI086871
    Consensus CDS
    CCDS31293.1
    UniProtKB/Swiss-Prot
    A0MZ66
    Related
    ENSP00000480109.1, ENST00000615301.4
    Conserved Domains (1) summary
    cl25732
    Location:140 → 350
    SMC_N; RecF/RecN/SMC N terminal domain

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    116881477..117126586 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    117775790..118020853 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A0MZ66.4 GenPept UniProtKB/Swiss-Prot:A0MZ66

Gene LinkOut

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

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Chemical Information
Molecular Biology Databases
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