Sema6b sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sema6bprovided by MGI
Official Full Name: sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Bprovided by MGI
Primary source: MGI:MGI:1202889
See related: Ensembl:ENSMUSG00000001227 AllianceGenome:MGI:1202889
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: VIb; Sema; Seman; semaZ
Summary: Enables semaphorin receptor binding activity. Involved in axon guidance and hippocampus development. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Is expressed in several structures, including genitourinary system; liver; musculature; spinal cord; and spleen. Human ortholog(s) of this gene implicated in progressive myoclonus epilepsy. Orthologous to human SEMA6B (semaphorin 6B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in frontal lobe adult (RPKM 19.8), cortex adult (RPKM 18.3) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 29.17 cM; 17 D

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (56430085..56447343, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (56123085..56140343, complement)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Class 6 transmembrane semaphorins are unlikely to serve as major PlexA receptor ligands for the assembly of murine retinal circuit laminar organization.
Title: Sema6B, Sema6C, and Sema6D expression and function during mammalian retinal development.
This study demonstrated that Sema6B, another class 6 transmembrane semaphorin, is expressed in CA3 and repels mossy fibers in a PlxnA4-dependent manner in vitro.
Title: Roles of semaphorin-6B and plexin-A2 in lamina-restricted projection of hippocampal mossy fibers.

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Variation

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Alleles

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

Targeted (1) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
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 axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	ISO Inferred from Sequence Orthology more info
involved_in hippocampus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
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 semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: semaphorin-6B

Names: sema N; sema VIB; semaphorin VIB; semaphorin-N

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_001130456.1 → NP_001123928.1 semaphorin-6B precursor

See identical proteins and their annotated locations for NP_001123928.1

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.

Source sequence(s)

AK139358, AK143229

Consensus CDS

CCDS28896.1

UniProtKB/Swiss-Prot

O54951

UniProtKB/TrEMBL

Q3TM84, Q3UTK5

Related

ENSMUSP00000001256.5, ENSMUST00000001256.11

Conserved Domains (3) summary

PHA03269
Location:708 → 875

PHA03269; envelope glycoprotein C; Provisional

cd11267
Location:58 → 526

Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)

smart00423
Location:527 → 573

PSI; domain found in Plexins, Semaphorins and Integrins
NM_013662.2 → NP_038690.1 semaphorin-6B precursor

See identical proteins and their annotated locations for NP_038690.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AK139358, BY082811

Consensus CDS

CCDS28896.1

UniProtKB/Swiss-Prot

O54951

UniProtKB/TrEMBL

Q3TM84, Q3UTK5

Related

ENSMUSP00000130985.2, ENSMUST00000167545.3

Conserved Domains (3) summary

PHA03269
Location:708 → 875

PHA03269; envelope glycoprotein C; Provisional

cd11267
Location:58 → 526

Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)

smart00423
Location:527 → 573

PSI; domain found in Plexins, Semaphorins and Integrins

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_000083.7 Reference GRCm39 C57BL/6J

Range

56430085..56447343 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006523930.5 → XP_006523993.1 semaphorin-6B isoform X1

See identical proteins and their annotated locations for XP_006523993.1

UniProtKB/Swiss-Prot

O54951

UniProtKB/TrEMBL

Q3TM84, Q3UTK5

Conserved Domains (3) summary

PHA03269
Location:708 → 875

PHA03269; envelope glycoprotein C; Provisional

cd11267
Location:58 → 526

Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)

smart00423
Location:527 → 573

PSI; domain found in Plexins, Semaphorins and Integrins