Sema6a semaphorin 6A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sema6aprovided by RGD
Official Full Name: semaphorin 6Aprovided by RGD
Primary source: RGD:1305493
See related: Ensembl:ENSRNOG00000004033 AllianceGenome:RGD:1305493
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable identical protein binding activity; signaling receptor binding activity; and transmembrane signaling receptor activity. Predicted to be involved in several processes, including generation of neurons; negative regulation of cell adhesion involved in sprouting angiogenesis; and negative regulation of signal transduction. Predicted to act upstream of or within cell surface receptor signaling pathway and centrosome localization. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA6A (semaphorin 6A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 118.1), Kidney (RPKM 79.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 18q11

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	18	NC_086036.1 (42237227..42358540, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	18	NC_051353.1 (40050623..40171954, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	18	NC_005117.4 (41330519..41451813, complement)

Chromosome 18 - NC_086036.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Semaphorin 6a overexpressed in the cortex enhances recovery after cerebral ischemia.
Title: Semaphorin 6A improves functional recovery in conjunction with motor training after cerebral ischemia.

Submit: New GeneRIF Correction

General gene information

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Markers

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

RH128795 (e-PCR)
- UniSTS:212103

RH133966 (e-PCR)
- UniSTS:217248

RH140065 (e-PCR)
- UniSTS:222146

RH139057 (e-PCR)
- UniSTS:221143

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	ISO Inferred from Sequence Orthology more info
enables transmembrane signaling receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cellular response to vascular endothelial growth factor stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within centrosome localization	ISO Inferred from Sequence Orthology more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of neuron migration	ISO Inferred from Sequence Orthology more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: semaphorin-6A

Names: sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A; 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_001108430.3 → NP_001101900.2 semaphorin-6A isoform 1 precursor

Status: VALIDATED

Description

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

Source sequence(s)

JAXUCZ010000018

UniProtKB/TrEMBL

A6IWY3, D3ZAG0

Related

ENSRNOP00000005476.7, ENSRNOT00000005476.9

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_001372354.2 → NP_001359283.1 semaphorin-6A isoform 2 precursor

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)

JAXUCZ010000018

UniProtKB/TrEMBL

A0A8I5ZYF8

Related

ENSRNOP00000082708.1, ENSRNOT00000115179.1

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086036.1 Reference GRCr8

Range

42237227..42358540 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063277473.1 → XP_063133543.1 semaphorin-6A isoform X3
XM_039096967.2 → XP_038952895.1 semaphorin-6A isoform X1

UniProtKB/TrEMBL

D3ZAX7

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
XM_003751782.6 → XP_003751830.1 semaphorin-6A isoform X1

See identical proteins and their annotated locations for XP_003751830.1

UniProtKB/TrEMBL

D3ZAX7

Related

ENSRNOP00000005446.5

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
XM_063277472.1 → XP_063133542.1 semaphorin-6A isoform X2

UniProtKB/TrEMBL

A6IWY3, D3ZAG0