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    SYNE3 spectrin repeat containing nuclear envelope family member 3 [ Homo sapiens (human) ]

    Gene ID: 161176, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SYNE3provided by HGNC
    Official Full Name
    spectrin repeat containing nuclear envelope family member 3provided by HGNC
    Primary source
    HGNC:HGNC:19861
    See related
    Ensembl:ENSG00000176438 MIM:610861; AllianceGenome:HGNC:19861
    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
    KASH3; NET53; Nesp3; C14orf49; C14orf139; LINC00341; NCRNA00341
    Summary
    Enables actin filament binding activity and cytoskeleton-nuclear membrane anchor activity. Involved in cytoskeleton organization; establishment of protein localization to membrane; and regulation of cell shape. Located in nuclear membrane. Part of meiotic nuclear membrane microtubule tethering complex. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in fat (RPKM 4.3), bone marrow (RPKM 3.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYNE3 in Genome Data Viewer
    Location:
    14q32.13
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (95407266..95516650, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (89637225..89747355, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (95873603..95982987, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370639 Neighboring gene uncharacterized LOC105370640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8958 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:95904894-95906093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95917656-95918448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95941052-95941938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95941939-95942824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95961573-95962074 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr14:95966308-95966888 and GRCh37_chr14:95966889-95967468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8962 Neighboring gene Sharpr-MPRA regulatory region 11978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8963 Neighboring gene SYNE3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 6741 Neighboring gene CRISPRi-validated cis-regulatory element chr14.2067 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:95999817-96000606 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:96000607-96001396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6049 Neighboring gene small Cajal body-specific RNA 13 Neighboring gene small nucleolar RNA host gene 10 Neighboring gene glutaredoxin 5

    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. Relationship between LINC00341 expression and cancer prognosis. Liao M, et al. Oncotarget, 2017 Feb 28. PMID 28146429, Free PMC Article
    2. Long Noncoding RNAs as Bone Marrow Stem Cell Regulators in Osteoporosis. Del Real A, et al. DNA Cell Biol, 2020 Sep. PMID 32700968
    3. Sperm‑associated antigen 4 (SPAG4) as a new cancer marker interacts with Nesprin3 to regulate cell migration in lung carcinoma. Ji Y, et al. Oncol Rep, 2018 Aug. PMID 29901114, Free PMC Article
    4. LINC00341 exerts an anti-inflammatory effect on endothelial cells by repressing VCAM1. Huang TS, et al. Physiol Genomics, 2017 Jul 1. PMID 28500253, Free PMC Article
    5. Nesprin-3, a novel outer nuclear membrane protein, associates with the cytoskeletal linker protein plectin. Wilhelmsen K, et al. J Cell Biol, 2005 Dec 5. PMID 16330710, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression profile of SYNE3 and bioinformatic analysis of its prognostic value and functions in tumors.
      Title: Expression profile of SYNE3 and bioinformatic analysis of its prognostic value and functions in tumors.
    2. Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes.
      Title: Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes.
    3. Long Noncoding RNAs as Bone Marrow Stem Cell Regulators in Osteoporosis.
      Title: Long Noncoding RNAs as Bone Marrow Stem Cell Regulators in Osteoporosis.
    4. LINC00341 interacts with miR-141 to suppress its functional binding to the 3'-untranslated region of YAF2 messenger RNA whereby supporting chondrocyte survival and preventing osteoarthritis progression.
      Title: A LINC00341-mediated regulatory pathway supports chondrocyte survival and may prevent osteoarthritis progression.
    5. SPAG4, in cooperation with Nesprin3, has a fundamental pathological function in the migration of lung carcinoma cells.
      Title: Sperm‑associated antigen 4 (SPAG4) as a new cancer marker interacts with Nesprin3 to regulate cell migration in lung carcinoma.
    6. Overexpression of LINC00341 suppresses the expression of vascular cell adhesion molecule 1 (VCAM1) and the adhesion of monocytes induced by atheroprone flow and tumor necrosis factor-alpha.
      Title: LINC00341 exerts an anti-inflammatory effect on endothelial cells by repressing VCAM1.
    7. Meta-analysis estimated the relationship between LINC00341 expression and distant metastasis or lymph node metastasis in breast cancer.
      Title: Relationship between LINC00341 expression and cancer prognosis.
    8. nesprin-3 regulates vascular endothelial cell shape, perinuclear cytoskeletal architecture, and important aspects of flow-mediated mechanotransduction.
      Title: Nesprin-3 regulates endothelial cell morphology, perinuclear cytoskeletal architecture, and flow-induced polarization.
    9. association with human nesprin-3 appeared to be stronger for torsinADeltaE than for torsinA. TorsinA also associated with the KASH domains of nesprin-1 and -2
      Title: TorsinA binds the KASH domain of nesprins and participates in linkage between nuclear envelope and cytoskeleton.
    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
    A genome-wide association study of survival in small-cell lung cancer patients treated with irinotecan plus cisplatin chemotherapy.
    EBI GWAS Catalog
    Genome-wide association study of sex hormones, gonadotropins and sex hormone-binding protein in Chinese men.
    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

    • FLJ21276, FLJ25605, MGC75267

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables actin filament binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables cytoskeleton-nuclear membrane anchor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in establishment of protein localization to membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nuclear migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cell shape IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of meiotic nuclear membrane microtubule tethering complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of meiotic nuclear membrane microtubule tethering complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nuclear outer membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in rough endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    nesprin-3
    Names
    KASH domain-containing protein 3
    long intergenic non-protein coding RNA 341
    nuclear envelope spectrin repeat protein 3
    uncharacterized protein C14orf113

    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_001363692.2 → NP_001350621.1  nesprin-3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL133467, AL138539
      Consensus CDS
      CCDS86430.1
      Related
      ENSP00000450562.1, ENST00000557275.5
      Conserved Domains (3) summary
      pfam10541
      Location:941 → 970
      KASH; Nuclear envelope localization domain
      cl02488
      Location:562 → 739
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cl25732
      Location:141 → 760
      SMC_N; RecF/RecN/SMC N terminal domain

    2. NM_001384281.1 → NP_001371210.1  nesprin-3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL133467, AL138539
      Consensus CDS
      CCDS91927.1
      Related
      ENSP00000450774.1, ENST00000553340.1
      Conserved Domains (1) summary
      TIGR02168
      Location:156 → 427
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    3. NM_001384282.1 → NP_001371211.1  nesprin-3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL133467, AL138539
      Consensus CDS
      CCDS91927.1
      Conserved Domains (1) summary
      TIGR02168
      Location:156 → 427
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    4. NM_001384283.1 → NP_001371212.1  nesprin-3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL133467, AL138539
      Conserved Domains (1) summary
      TIGR02168
      Location:164 → 435
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    5. NM_001384284.1 → NP_001371213.1  nesprin-3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL133467, AL138539
      Conserved Domains (1) summary
      TIGR02168
      Location:156 → 427
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    6. NM_152592.6 → NP_689805.3  nesprin-3 isoform 1

      See identical proteins and their annotated locations for NP_689805.3

      Status: VALIDATED

      Source sequence(s)
      AL133467, AL138539
      Consensus CDS
      CCDS9935.1
      UniProtKB/Swiss-Prot
      A6H8H3, Q6ZMZ3, Q86SX5, Q8N7G8
      Related
      ENSP00000507501.1, ENST00000682763.1
      Conserved Domains (3) summary
      TIGR02168
      Location:141 → 760
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam10541
      Location:946 → 975
      KASH; Nuclear envelope localization domain
      cl02488
      Location:562 → 739
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      95407266..95516650 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      89637225..89747355 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_024633.2: Suppressed sequence

      Description
      NM_024633.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZMZ3.2 GenPept UniProtKB/Swiss-Prot:Q6ZMZ3

    Gene LinkOut

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

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