Nectin1 nectin cell adhesion molecule 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nectin1provided by RGD
Official Full Name: nectin cell adhesion molecule 1provided by RGD
Primary source: RGD:620791
See related: Ensembl:ENSRNOG00000006403 AllianceGenome:RGD:620791
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
Also known as: HveC; Pvrl1; nectin-1
Summary: Enables carbohydrate binding activity and virion binding activity. Involved in axon guidance; regulation of synapse assembly; and viral entry into host cell. Located in several cellular components, including dendrite; growth cone membrane; and synapse. Human ortholog(s) of this gene implicated in cleft lip; cleft lip-palate-ectodermal dysplasia syndrome; cleft palate; and ectodermal dysplasia. Orthologous to human NECTIN1 (nectin cell adhesion molecule 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 45.4), Brain (RPKM 31.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q22

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (52998662..53061745)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (44101776..44164863)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (48094233..48198499)

Chromosome 8 - NC_086026.1 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?

Data indicate that contextual fear conditioning showed transient nectin-1 upregulation in synapse-enriched hippocampal fractions at about 2 h posttraining.
Title: A key role for nectin-1 in the ventral hippocampus in contextual fear memory.
primary receptor for HSV-1 infection of rat sensory neurons
Title: Entry of herpes simplex virus type 1 into primary sensory neurons in vitro is mediated by Nectin-1/HveC.

Submit: New GeneRIF Correction

General gene information

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Markers

BE121372 (e-PCR)
- UniSTS:248073

AW529741 (e-PCR)
- UniSTS:261233

BI274299 (e-PCR)
- UniSTS:249060

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables carbohydrate binding	IDA Inferred from Direct Assay more info	PubMed
enables cell adhesion molecule binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables signaling receptor activity	ISO Inferred from Sequence Orthology more info
enables virion binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell-cell adhesion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within desmosome organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within enamel mineralization	ISO Inferred from Sequence Orthology more info
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	ISO Inferred from Sequence Orthology more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within iron ion transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lens morphogenesis in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in protein localization to cell junction	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein localization to cell junction	ISO Inferred from Sequence Orthology more info
involved_in regulation of synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synapse organization	EXP Inferred from Experiment more info	PubMed
involved_in regulation of synapse organization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in symbiont entry into host cell	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	ISO Inferred from Sequence Orthology more info
located_in apical junction complex	ISO Inferred from Sequence Orthology more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cell-cell contact zone	ISO Inferred from Sequence Orthology more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in growth cone membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in hippocampal mossy fiber to CA3 synapse	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic active zone membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nectin-1

Names: nectin); poliovirus receptor-related 1 (herpesvirus entry mediator C; poliovirus receptor-related 1 (herpesvirus entry mediator C; nectin); poliovirus receptor-related protein 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_001100476.1 → NP_001093946.1 nectin-1 precursor

See identical proteins and their annotated locations for NP_001093946.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

A6J3U6, F1LNP8

Related

ENSRNOP00000008614.6, ENSRNOT00000008614.8

Conserved Domains (5) summary

cd05890
Location:146 → 243

IgC1_2_Nectin-1_like; Second immunoglobulin (Ig) domain of nectin-1, and similar domains; member of the C1-set of Ig superfamily (IgSF) domains

pfam14575
Location:355 → 401

EphA2_TM; Ephrin type-A receptor 2 transmembrane domain

cd00096
Location:247 → 253

Ig; Ig strand A [structural motif]

cd05886
Location:31 → 143

IgV_1_Nectin-1_like; First immunoglobulin variable (IgV) domain of nectin-1, and similar domains

cl11960
Location:247 → 333

Ig; Immunoglobulin domain