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SEMA5B semaphorin 5B [ Homo sapiens (human) ]

Gene ID: 54437, updated on 22-Aug-2020

Summary

Official Symbol
SEMA5Bprovided by HGNC
Official Full Name
semaphorin 5Bprovided by HGNC
Primary source
HGNC:HGNC:10737
See related
Ensembl:ENSG00000082684 MIM:609298
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
SemG; SEMAG
Summary
This gene encodes a member of the semaphorin protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
Expression
Broad expression in brain (RPKM 2.8), heart (RPKM 1.3) and 16 other tissues See more
Orthologs

Genomic context

See SEMA5B in Genome Data Viewer
Location:
3q21.1
Exon count:
26
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (122909082..123028605, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (122628040..122747452, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene HSPB1 associated protein 1 Neighboring gene solute carrier family 49 member 4 Neighboring gene long intergenic non-protein coding RNA 2035 Neighboring gene uncharacterized LOC112268448 Neighboring gene protein disulfide isomerase family A member 5 Neighboring gene microRNA 7110 Neighboring gene SEC22 homolog A, vesicle trafficking protein

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?

Phenotypes

Associated conditions

Description Tests
Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations.
GeneReviews: Not available

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of sema domain, 5B (SEMA5B) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10372, KIAA1445

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
axon extension IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
detection of light stimulus involved in visual perception IEA
Inferred from Electronic Annotation
more info
 
negative chemotaxis IEA
Inferred from Electronic Annotation
more info
 
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
integral component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
semaphorin-5B
Names
sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B

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.

mRNA and Protein(s)

  1. NM_001031702.4NP_001026872.2  semaphorin-5B isoform 1

    See identical proteins and their annotated locations for NP_001026872.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    AB040878, AC078794, AK091481, BC002776, BC077726, DA115188, DA797213
    Consensus CDS
    CCDS35491.1
    UniProtKB/Swiss-Prot
    Q9P283
    Related
    ENSP00000350215.3, ENST00000357599.8
    Conserved Domains (4) summary
    cd11264
    Location:118554
    Sema_5B; The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)
    smart00209
    Location:856908
    TSP1; Thrombospondin type 1 repeats
    pfam00090
    Location:9691010
    TSP_1; Thrombospondin type 1 domain
    pfam01437
    Location:555602
    PSI; Plexin repeat
  2. NM_001256346.2NP_001243275.1  semaphorin-5B isoform 1

    See identical proteins and their annotated locations for NP_001243275.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    AC078794, AC109130, AK091481
    Consensus CDS
    CCDS35491.1
    UniProtKB/Swiss-Prot
    Q9P283
    Related
    ENSP00000479602.1, ENST00000616742.4
    Conserved Domains (4) summary
    cd11264
    Location:118554
    Sema_5B; The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)
    smart00209
    Location:856908
    TSP1; Thrombospondin type 1 repeats
    pfam00090
    Location:9691010
    TSP_1; Thrombospondin type 1 domain
    pfam01437
    Location:555602
    PSI; Plexin repeat
  3. NM_001256347.1NP_001243276.1  semaphorin-5B isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding region and uses an alternate start codon compared to variant 1. The resulting protein (isoform 2) has a longer N-terminus compared to isoform 1.
    Source sequence(s)
    AC078794, AC109130, AK295619
    Consensus CDS
    CCDS58848.1
    UniProtKB/Swiss-Prot
    Q9P283
    Related
    ENSP00000389588.2, ENST00000451055.6
    Conserved Domains (4) summary
    cd11264
    Location:172608
    Sema_5B; The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)
    smart00209
    Location:910962
    TSP1; Thrombospondin type 1 repeats
    pfam00090
    Location:10231064
    TSP_1; Thrombospondin type 1 domain
    pfam01437
    Location:609656
    PSI; Plexin repeat
  4. NM_001256348.2NP_001243277.1  semaphorin-5B isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, uses a downstream start codon and uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 3) is shorter and has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC078794, AC083797, AK294528
    Consensus CDS
    CCDS74995.1
    UniProtKB/TrEMBL
    B7Z2B3, C9JKR3
    Related
    ENSP00000195173.5, ENST00000195173.8
    Conserved Domains (4) summary
    cd11264
    Location:60496
    Sema_5B; The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)
    smart00209
    Location:798850
    TSP1; Thrombospondin type 1 repeats
    pfam00090
    Location:875916
    TSP_1; Thrombospondin type 1 domain
    pfam01437
    Location:497544
    PSI; Plexin repeat

RNA

  1. NR_046079.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) has an alternate 5' exon and uses an alternate splice site 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)
    AC078794, AY358124

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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
    122909082..123028605 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006638.2XP_016862127.1  semaphorin-5B isoform X1

    Related
    ENSP00000496878.1, ENST00000650207.1
  2. XM_017006639.1XP_016862128.1  semaphorin-5B isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_018987.1: Suppressed sequence

    Description
    NM_018987.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate and has no publication or homolog support.
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