Sema6a sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sema6aprovided by MGI
Official Full Name: sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Aprovided by MGI
Primary source: MGI:MGI:1203727
See related: Ensembl:ENSMUSG00000019647 AllianceGenome:MGI:1203727
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: VIa; Semaq; Sema6A-1; A730020P05Rik
Summary: Enables identical protein binding activity; semaphorin receptor binding activity; and transmembrane signaling receptor activity. Involved in generation of neurons; positive regulation of neuron migration; and semaphorin-plexin signaling pathway. Acts upstream of or within cell surface receptor signaling pathway and centrosome localization. Located in plasma membrane. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and sensory organ. Orthologous to human SEMA6A (semaphorin 6A). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in limb E14.5 (RPKM 13.8), lung adult (RPKM 13.8) and 23 other tissues See more
Orthologs: human all
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Genomic context

Location:: 18 C; 18 25.08 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	18	NC_000084.7 (47378321..47504267, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	18	NC_000084.6 (47245254..47371200, complement)

Chromosome 18 - NC_000084.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structural basis of semaphorin-plexin cis interaction.
Title: Structural basis of semaphorin-plexin cis interaction.
Recognition of Semaphorin Proteins by P. sordellii Lethal Toxin Reveals Principles of Receptor Specificity in Clostridial Toxins.
Title: Recognition of Semaphorin Proteins by P. sordellii Lethal Toxin Reveals Principles of Receptor Specificity in Clostridial Toxins.
Study shows remarkable complexity and variability of corticospinal tract defects in adult Semaphorin 6A knockout mice.
Title: Remarkable complexity and variability of corticospinal tract defects in adult Semaphorin 6A knockout mice.
Data show that opposing effects of neurotrophic brain-derived neurotrophic factor (BDNF) and repulsive Sema6a Semaphorins (Sema6a) factors regulate the sensory innervation of the mammary gland.
Title: Balance between BDNF and Semaphorins gates the innervation of the mammary gland.
We find that the transmembrane protein semaphorin 6A (Sema6A) is required for the formation of axonal projections from the medial terminal nucleus to the nucleus of the optic tract
Title: Genetic access to neurons in the accessory optic system reveals a role for Sema6A in midbrain circuitry mediating motion perception.
These findings implicate Semaphorin-6A - Plexin-A2/Plexin-A4 interactions in dorsal lateral geniculate nucleus axon guidance and in the spatiotemporal organization of guidepost cell populations in the mammalian subpallium.
Title: Semaphorin-Plexin signaling influences early ventral telencephalic development and thalamocortical axon guidance.
Shear stress-regulated miR-27b promotes the interaction of endothelial cells with pericytes, partly by repressing SEMA6A and SEMA6D.
Title: Shear stress-regulated miR-27b controls pericyte recruitment by repressing SEMA6A and SEMA6D.
mutations in Sema6A, and/or possibly interacting genes, may result in dysfunction at the level of neuronal networks with associated behavioural phenotypes of relevance to neuropsychiatric disorders
Title: Semaphorin 6A knockout mice display abnormalities across ethologically-based topographies of exploration and in motor learning.
The experiments reveal the complex nature of Sema6A biochemical functions and the molecular logic of the context-dependent interactions between Sema6A and PlxnA2.
Title: Reverse Signaling by Semaphorin-6A Regulates Cellular Aggregation and Neuronal Morphology.
Using time-lapse videomicroscopy we provide evidence that Sema6A/PlexinA2 signaling participates to interkinetic nuclear migration of retinal progenitor cell
Title: PlexinA2 and Sema6A are required for retinal progenitor cell migration.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5)
Gene trapped (1) 1 citation
Targeted (10) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D18Mit179 (e-PCR), detects polymorphism
- UniSTS:116802

STS-N27270 (e-PCR)
- UniSTS:20815

AI851735 (e-PCR)
- UniSTS:181115

px-57f8 (e-PCR)
- UniSTS:257957

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IGI Inferred from Genetic Interaction more info	PubMed
enables semaphorin receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane signaling receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in apoptotic process	NAS Non-traceable Author Statement more info	PubMed
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axon guidance	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within cell surface receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to vascular endothelial growth factor stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within centrosome localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell adhesion involved in sprouting angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of sprouting angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of vascular endothelial growth factor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axon	NAS Non-traceable Author Statement more info	PubMed
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: semaphorin-6A

Names: Mutant line 997; sema Q; sema VIA; semaphorin Q; semaphorin VIA; semaphorin-6A-1

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)

NM_001311097.1 → NP_001298026.1 semaphorin-6A isoform 2 precursor

See identical proteins and their annotated locations for NP_001298026.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC121783, AC124466, AI606937, AK034123, AK082711, BC059238, BC062979

Consensus CDS

CCDS79642.1

Related

ENSMUSP00000075420.7, ENSMUST00000076043.13

Conserved Domains (2) summary

cd11266
Location:48 → 513

Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)

pfam01437
Location:514 → 544

PSI; Plexin repeat
NM_018744.2 → NP_061214.2 semaphorin-6A isoform 1 precursor

See identical proteins and their annotated locations for NP_061214.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC124466, AI606937, AK042751, BC059238

Consensus CDS

CCDS37813.1

UniProtKB/Swiss-Prot

O35464, Q6P5A8, Q6PCN9, Q9EQ71

Related

ENSMUSP00000019791.8, ENSMUST00000019791.14

Conserved Domains (2) summary

cd11266
Location:48 → 513

Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)

pfam01437
Location:514 → 544

PSI; Plexin repeat

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000084.7 Reference GRCm39 C57BL/6J

Range

47378321..47504267 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006525726.2 → XP_006525789.1 semaphorin-6A isoform X1

See identical proteins and their annotated locations for XP_006525789.1

UniProtKB/TrEMBL

D3YWM8

Related

ENSMUSP00000120011.2, ENSMUST00000135790.8

Conserved Domains (2) summary

cd11266
Location:48 → 513

Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)

pfam01437
Location:514 → 546

PSI; Plexin repeat
XM_006525727.5 → XP_006525790.1 semaphorin-6A isoform X1

See identical proteins and their annotated locations for XP_006525790.1

UniProtKB/TrEMBL

D3YWM8

Conserved Domains (2) summary

cd11266
Location:48 → 513

Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)

pfam01437
Location:514 → 546

PSI; Plexin repeat