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    SEMA3E semaphorin 3E [ Homo sapiens (human) ]

    Gene ID: 9723, updated on 9-Dec-2024

    Summary

    Official Symbol
    SEMA3Eprovided by HGNC
    Official Full Name
    semaphorin 3Eprovided by HGNC
    Primary source
    HGNC:HGNC:10727
    See related
    Ensembl:ENSG00000170381 MIM:608166; AllianceGenome:HGNC:10727
    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
    SEMAH; coll-5; M-SEMAH; M-SemaK
    Summary
    Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. This gene encodes a class 4 semaphorin. This gene encodes a class 3 semaphorin. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]
    Expression
    Biased expression in brain (RPKM 3.1), gall bladder (RPKM 2.2) and 13 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SEMA3E in Genome Data Viewer
    Location:
    7q21.11
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (83363238..83649139, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (84614452..84899593, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (82992554..83278455, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene piccolo presynaptic cytomatrix protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:82653064-82653634 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:82653635-82654203 Neighboring gene RNA, 5S ribosomal pseudogene 235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26214 Neighboring gene uncharacterized LOC105375377 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:82833944-82834566 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:82840511-82841088 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:82841089-82841665 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83088278-83089221 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83089222-83090164 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:83093938-83094880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26215 Neighboring gene uncharacterized LOC105375378 Neighboring gene NANOG hESC enhancer GRCh37_chr7:83126208-83126709 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83314287-83314786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83315470-83315977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:83320326-83320837 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:83322516-83323158 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:83337804-83339003 Neighboring gene RAD23B pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26217 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83463173-83463673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18337 Neighboring gene uncharacterized LOC107986745

    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

    Related articles in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies new susceptibility loci for epithelial ovarian cancer in Han Chinese women.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of sema domain, immunoglobulin domain, short basic domain, secreted, 3E (SEMA3E) in primary human brain microvascular endothelial cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0331

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables receptor ligand activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables semaphorin receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in branching involved in blood vessel morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cell-matrix adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of neuron apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of cell shape IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in semaphorin-plexin signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in semaphorin-plexin signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sprouting angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synapse organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    semaphorin-3E
    Names
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E

    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.

    Genomic

    1. NG_021242.2 RefSeqGene

      Range
      5025..290926
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1287

    mRNA and Protein(s)

    1. NM_001178129.2NP_001171600.1  semaphorin-3E isoform 2

      See identical proteins and their annotated locations for NP_001171600.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC079799, AK303925, BC152458
      UniProtKB/TrEMBL
      B4DLY1
      Conserved Domains (3) summary
      cd05871
      Location:525610
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11253
      Location:1459
      Sema_3E; The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E)
      smart00423
      Location:458506
      PSI; domain found in Plexins, Semaphorins and Integrins
    2. NM_012431.3NP_036563.1  semaphorin-3E isoform 1 precursor

      See identical proteins and their annotated locations for NP_036563.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC079799, AW450461, BC140706, BC152458, DA722912, DB215551
      Consensus CDS
      CCDS34674.1
      UniProtKB/Swiss-Prot
      B4E1P1, O15041, Q75M94, Q75M97
      UniProtKB/TrEMBL
      B4DLY1
      Related
      ENSP00000496491.1, ENST00000643230.2
      Conserved Domains (3) summary
      cd05871
      Location:585670
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11253
      Location:49519
      Sema_3E; The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E)
      smart00423
      Location:518566
      PSI; domain found in Plexins, Semaphorins and Integrins

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      83363238..83649139 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      84614452..84899593 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)