SEMA5A semaphorin 5A [Homo sapiens (human)] - Gene

Summary

Official Symbol: SEMA5Aprovided by HGNC
Official Full Name: semaphorin 5Aprovided by HGNC
Primary source: HGNC:HGNC:10736
See related: Ensembl:ENSG00000112902 MIM:609297; AllianceGenome:HGNC:10736
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: semF; SEMAF
Summary: This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]
Expression: Broad expression in lung (RPKM 6.9), kidney (RPKM 6.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5p15.31

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (9035033..9546075, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (8974898..9485916, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (9035145..9546187, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Circular RNA circSEMA5A facilitates colorectal cancer development by regulating microRNA-195-5p to target CCNE1 axis.
Title: Circular RNA circSEMA5A facilitates colorectal cancer development by regulating microRNA-195-5p to target CCNE1 axis.
SEMA5A-PLXNB3 Axis Promotes PDAC Liver Metastasis Outgrowth through Enhancing the Warburg Effect.
Title: SEMA5A-PLXNB3 Axis Promotes PDAC Liver Metastasis Outgrowth through Enhancing the Warburg Effect.
Semaphorin 5A suppresses ferroptosis through activation of PI3K-AKT-mTOR signaling in rheumatoid arthritis.
Title: Semaphorin 5A suppresses ferroptosis through activation of PI3K-AKT-mTOR signaling in rheumatoid arthritis.
TSP1 is the essential domain of SEMA5A involved in pannus formation in rheumatoid arthritis.
Title: TSP1 is the essential domain of SEMA5A involved in pannus formation in rheumatoid arthritis.
Relationship between disease and disease severity and semaphorin 5A and hemogram level in obsessive-compulsive disorder.
Title: Relationship between disease and disease severity and semaphorin 5A and hemogram level in obsessive-compulsive disorder.
The Expression of IL-17, in Chronic Spontaneous Urticaria Is Linked to Semaphorin5A.
Title: The Expression of IL-17, in Chronic Spontaneous Urticaria Is Linked to Semaphorin5A.
Circular RNA circSEMA5A promotes bladder cancer progression by upregulating ENO1 and SEMA5A expression.
Title: Circular RNA circSEMA5A promotes bladder cancer progression by upregulating ENO1 and SEMA5A expression.
Semaphorin 5A suppresses the proliferation and migration of lung adenocarcinoma cells.
Title: Semaphorin 5A suppresses the proliferation and migration of lung adenocarcinoma cells.
High Expression Levels of Long Noncoding RNA Small Nucleolar RNA Host Gene 18 and Semaphorin 5A Indicate Poor Prognosis in Multiple Myeloma.
Title: High Expression Levels of Long Noncoding RNA Small Nucleolar RNA Host Gene 18 and Semaphorin 5A Indicate Poor Prognosis in Multiple Myeloma.
Semaphorin-5A downregulation is associated with enhanced migration and invasion of BRAF-positive melanoma cells under vemurafenib treatment in melanomas with heterogeneous BRAF status
Title: Semaphorin-5A downregulation is associated with enhanced migration and invasion of BRAF-positive melanoma cells under vemurafenib treatment in melanomas with heterogeneous BRAF status.

Submit: New GeneRIF Correction See all GeneRIFs (39)

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 linkage and association scan reveals novel loci for autism. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association of serum uric acid concentration: replication of sequence variants in an island population of the Adriatic coast of Croatia. EBI GWAS Catalog EBI GWAS CatalogPubMed
High-resolution whole-genome association study of Parkinson disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

General gene information

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Markers

D5S1880 (e-PCR)
- UniSTS:19210

STS-U10508 (e-PCR)
- UniSTS:80672

SHGC-149507 (e-PCR)
- UniSTS:184100

RH92606 (e-PCR)
- UniSTS:88873

D5S2095 (e-PCR), detects polymorphism
- UniSTS:19265

G20633 (e-PCR)
- UniSTS:6737

A005Z39 (e-PCR)
- UniSTS:6738

RH12734 (e-PCR)
- UniSTS:20847

RH45272 (e-PCR)
- UniSTS:50299

RH46269 (e-PCR)
- UniSTS:29587

SEMA5A_1487 (e-PCR)
- UniSTS:280990

D5S807 (e-PCR), detects polymorphism
- UniSTS:70568

RH65788 (e-PCR)
- UniSTS:47283

RH122478 (e-PCR)
- UniSTS:135351

D5S1512E (e-PCR)
- UniSTS:149976

D5S1514E (e-PCR)
- UniSTS:149978

D5S1515E (e-PCR)
- UniSTS:149979

D5S1516E (e-PCR)
- UniSTS:149980

D5S1518E (e-PCR)
- UniSTS:149982

SHGC-149224 (e-PCR)
- UniSTS:176873

D5S1842 (e-PCR)
- UniSTS:38908

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables chondroitin sulfate proteoglycan binding	ISS Inferred from Sequence or Structural Similarity more info
enables heparan sulfate proteoglycan binding	ISS Inferred from Sequence or Structural Similarity more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables semaphorin receptor binding	ISS Inferred from Sequence or Structural Similarity more info
enables syndecan binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in axon extension	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in axonal fasciculation	ISS Inferred from Sequence or Structural Similarity more info
involved_in blood vessel endothelial cell proliferation involved in sprouting angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in cell chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in diencephalon development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of axon extension involved in axon guidance	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of axon extension involved in axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of endothelial cell apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of actin filament depolymerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of axon extension involved in axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of canonical Wnt signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of endothelial cell chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of endothelial cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in signal clustering	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: semaphorin-5A

Names: sema F; sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A; semaphorin F

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.

Genomic

NG_016410.2 RefSeqGene

Range

5000..516042

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_003966.3 → NP_003957.2 semaphorin-5A precursor

See identical proteins and their annotated locations for NP_003957.2

Status: REVIEWED

Source sequence(s)

AC021088, AC022446, AC027335, AC027336, AC034214, AC091906

Consensus CDS

CCDS3875.1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95

Related

ENSP00000371936.5, ENST00000382496.10

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:844 → 896

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

9035033..9546075 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011514158.3 → XP_011512460.1 semaphorin-5A isoform X1

See identical proteins and their annotated locations for XP_011512460.1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:844 → 896

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_011514157.3 → XP_011512459.1 semaphorin-5A isoform X1

See identical proteins and their annotated locations for XP_011512459.1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:844 → 896

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_006714506.4 → XP_006714569.1 semaphorin-5A isoform X1

See identical proteins and their annotated locations for XP_006714569.1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:844 → 896

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_011514156.3 → XP_011512458.1 semaphorin-5A isoform X1

See identical proteins and their annotated locations for XP_011512458.1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95

Related

ENSP00000499013.1, ENST00000652226.1

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:844 → 896

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_011514155.3 → XP_011512457.1 semaphorin-5A isoform X1

See identical proteins and their annotated locations for XP_011512457.1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:844 → 896

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_047417865.1 → XP_047273821.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95
XM_047417866.1 → XP_047273822.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95
XM_006714507.4 → XP_006714570.1 semaphorin-5A isoform X1

See identical proteins and their annotated locations for XP_006714570.1

UniProtKB/Swiss-Prot

D3DTC6, O60408, Q13591, Q1RLL9

UniProtKB/TrEMBL

X5DR95

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:844 → 896

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_047417867.1 → XP_047273823.1 semaphorin-5A isoform X3
XM_011514159.3 → XP_011512461.1 semaphorin-5A isoform X2

Conserved Domains (3) summary

smart00209
Location:797 → 849

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:439 → 486

PSI; Plexin repeat

cl15693
Location:34 → 438

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins