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SEMA3B semaphorin 3B [ Homo sapiens (human) ]

Gene ID: 7869, updated on 21-Jan-2020

Summary

Official Symbol
SEMA3Bprovided by HGNC
Official Full Name
semaphorin 3Bprovided by HGNC
Primary source
HGNC:HGNC:10724
See related
Ensembl:ENSG00000012171 MIM:601281
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
SemA; SEMA5; SEMAA; semaV; LUCA-1
Summary
The protein encoded by this gene belongs to the class-3 semaphorin/collapsin family, whose members function in growth cone guidance during neuronal development. This family member inhibits axonal extension and has been shown to act as a tumor suppressor by inducing apoptosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]
Expression
Broad expression in placenta (RPKM 31.6), small intestine (RPKM 29.6) and 20 other tissues See more
Orthologs

Genomic context

See SEMA3B in Genome Data Viewer
Location:
3p21.31
Exon count:
18
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (50267558..50277546)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50305040..50314573)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene microRNA 5787 Neighboring gene G protein subunit alpha i2 Neighboring gene SEMA3B antisense RNA 1 (head to head) Neighboring gene microRNA 6872 Neighboring gene leucine rich single-pass membrane protein 2 Neighboring gene interferon related developmental regulator 2 Neighboring gene hyaluronidase 3 Neighboring gene N-alpha-acetyltransferase 80, NatH catalytic subunit

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34863

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemorepellent activity TAS
Traceable Author Statement
more info
PubMed 
semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
axon guidance TAS
Traceable Author Statement
more info
PubMed 
cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
chemorepulsion of axon TAS
Traceable Author Statement
more info
PubMed 
negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
collagen-containing extracellular matrix HDA PubMed 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
semaphorin-3B
Names
sema A(V)
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B
semaphorin A
semaphorin-V

NCBI Reference Sequences (RefSeq)

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_032938.1 RefSeqGene

    Range
    4951..14564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001005914.2NP_001005914.1  semaphorin-3B isoform 2 precursor

    See identical proteins and their annotated locations for NP_001005914.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1. The 5' terminal exon of this variant is inferred based on tiled partial transcript alignments.
    Source sequence(s)
    AI309508, BC009113, BC013975, HY146744
    Consensus CDS
    CCDS77744.1
    UniProtKB/Swiss-Prot
    Q13214
    Related
    ENSP00000485281.1, ENST00000433753.4
    Conserved Domains (3) summary
    cd05871
    Location:574664
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    smart00423
    Location:514550
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl15693
    Location:46515
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  2. NM_001290060.2NP_001276989.1  semaphorin-3B isoform 1 precursor

    See identical proteins and their annotated locations for NP_001276989.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode isoform 1.
    Source sequence(s)
    AI309508, BC009113, U28369, U90094
    Consensus CDS
    CCDS74941.1
    UniProtKB/Swiss-Prot
    Q13214
    Related
    ENSP00000484146.1, ENST00000616701.5
    Conserved Domains (3) summary
    cd05871
    Location:575665
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11250
    Location:46516
    Sema_3B; The Sema domain, a protein interacting module, of semaphorin 3B (Sema3B)
    smart00423
    Location:515551
    PSI; domain found in Plexins, Semaphorins and Integrins
  3. NM_001290061.1NP_001276990.1  semaphorin-3B isoform 3 precursor

    See identical proteins and their annotated locations for NP_001276990.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
    Source sequence(s)
    AB083186, AI309508, BC009113, HY146744
    Consensus CDS
    CCDS77743.1
    UniProtKB/Swiss-Prot
    Q13214
    UniProtKB/TrEMBL
    A0A0C4DGV8
    Related
    ENSP00000480680.1, ENST00000611067.4
    Conserved Domains (3) summary
    cd05871
    Location:580670
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    smart00423
    Location:520556
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl15693
    Location:46521
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  4. NM_001290062.1NP_001276991.1  semaphorin-3B isoform 4

    See identical proteins and their annotated locations for NP_001276991.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks several 5' exons but contains alternate 5' exon structure, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 6 encode isoform 4.
    Source sequence(s)
    AI309508, AK293678, BC009113, BC044602, DC330072
    Consensus CDS
    CCDS77745.1
    UniProtKB/Swiss-Prot
    Q13214
    UniProtKB/TrEMBL
    B4DEK9, Q6PI51
    Related
    ENSP00000485646.1, ENST00000456560.6
    Conserved Domains (3) summary
    smart00423
    Location:172208
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:232322
    Ig; Immunoglobulin domain
    cl15693
    Location:1173
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  5. NM_001290063.1NP_001276992.1  semaphorin-3B isoform 4

    See identical proteins and their annotated locations for NP_001276992.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks several 5' exons but contains alternate 5' exon structure, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 6 encode isoform 4.
    Source sequence(s)
    AI309508, AK293678, BC009113, DC330072
    Consensus CDS
    CCDS77745.1
    UniProtKB/Swiss-Prot
    Q13214
    UniProtKB/TrEMBL
    B4DEK9
    Related
    ENSP00000485173.1, ENST00000418576.3
    Conserved Domains (3) summary
    smart00423
    Location:172208
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:232322
    Ig; Immunoglobulin domain
    cl15693
    Location:1173
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  6. NM_004636.3NP_004627.1  semaphorin-3B isoform 1 precursor

    See identical proteins and their annotated locations for NP_004627.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. Both variants 1 and 3 encode isoform 1. The 5' terminal exon of this variant is inferred based on tiled partial transcript alignments.
    Source sequence(s)
    AI309508, BC009113, HY146744, U28369
    Consensus CDS
    CCDS74941.1
    UniProtKB/Swiss-Prot
    Q13214
    Related
    ENSP00000481957.1, ENST00000618865.4
    Conserved Domains (3) summary
    cd05871
    Location:575665
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11250
    Location:46516
    Sema_3B; The Sema domain, a protein interacting module, of semaphorin 3B (Sema3B)
    smart00423
    Location:515551
    PSI; domain found in Plexins, Semaphorins and Integrins

RNA

  1. NR_110697.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks several 5' exons but contains alternate 5' exon structure, and it also lacks three internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI309508, AK092182, BC009113, DC330072
    Related
    ENST00000456210.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    50267558..50277546
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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