Plxnc1 plexin C1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Plxnc1provided by RGD
Official Full Name: plexin C1provided by RGD
Primary source: RGD:1307420
See related: Ensembl:ENSRNOG00000007970 AllianceGenome:RGD:1307420
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 semaphorin receptor activity. Predicted to be involved in several processes, including generation of neurons; regulation of GTPase activity; and regulation of cell shape. Predicted to be part of semaphorin receptor complex. Predicted to be integral component of plasma membrane. Orthologous to human PLXNC1 (plexin C1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 116.3), Spleen (RPKM 95.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q13

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (31276978..31430823, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (29390038..29543985, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (35848083..36000969, complement)

Chromosome 7 - NC_086025.1 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: 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?

SEMA7A promotes seawater induced lung edema via plexin C1 and stimulates seawater induced lung inflammation via beta1 integrin.
Title: Endothelial semaphorin 7A promotes seawater aspiration-induced acute lung injury through plexin C1 and β1 integrin.
Sema7A and plexinC1 expression patterns are consistent with these proteins serving both cooperative and separate functions during neural development
Title: Expression patterns of semaphorin7A and plexinC1 during rat neural development suggest roles in axon guidance and neuronal migration.

Submit: New GeneRIF Correction

General gene information

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Markers

BE102511 (e-PCR)
- UniSTS:244230

BE117374 (e-PCR)
- UniSTS:248669

BF390429 (e-PCR)
- UniSTS:249465

RH132911 (e-PCR)
- UniSTS:216194

WI-14237 (e-PCR)
- UniSTS:11724

Plxnc1 (e-PCR), detects polymorphism
- UniSTS:507885

D7Rat27 (e-PCR)
- UniSTS:119029

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables semaphorin receptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in negative regulation of cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell shape	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of synapse pruning	ISO Inferred from Sequence Orthology more info
involved_in semaphorin-plexin signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cerebellar climbing fiber to Purkinje cell synapse	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of semaphorin receptor complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: plexin-C1

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_001426988.1 → NP_001413917.1 plexin-C1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

A0A8I5ZKT8

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_086025.1 Reference GRCr8

Range

31276978..31430823 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039080100.2 → XP_038936028.2 plexin-C1 isoform X1
XM_039080102.2 → XP_038936030.1 plexin-C1 isoform X4

Conserved Domains (4) summary

smart00429
Location:204 → 296

IPT; ig-like, plexins, transcription factors

pfam01437
Location:39 → 83

PSI; Plexin repeat

pfam01833
Location:115 → 201

TIG; IPT/TIG domain

pfam08337
Location:467 → 990

Plexin_cytopl; Plexin cytoplasmic RasGAP domain
XM_039080103.2 → XP_038936031.1 plexin-C1 isoform X4

Conserved Domains (4) summary

smart00429
Location:204 → 296

IPT; ig-like, plexins, transcription factors

pfam01437
Location:39 → 83

PSI; Plexin repeat

pfam01833
Location:115 → 201

TIG; IPT/TIG domain

pfam08337
Location:467 → 990

Plexin_cytopl; Plexin cytoplasmic RasGAP domain
XM_039080101.2 → XP_038936029.2 plexin-C1 isoform X2
XM_063263772.1 → XP_063119842.1 plexin-C1 isoform X3

RNA

XR_005486861.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001108744.1: Suppressed sequence

Description

NM_001108744.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: PLXNC1 (GeneID:10154).