Lypd1 Ly6/Plaur domain containing 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lypd1provided by RGD
Official Full Name: Ly6/Plaur domain containing 1provided by RGD
Primary source: RGD:1549754
See related: Ensembl:ENSRNOG00000003453 AllianceGenome:RGD:1549754
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Lypdc1
Summary: Predicted to enable acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Predicted to be involved in acetylcholine receptor signaling pathway. Predicted to act upstream of or within several processes, including behavioral fear response; cholinergic synaptic transmission; and negative regulation of protein localization to plasma membrane. Predicted to be located in membrane. Orthologous to human LYPD1 (LY6/PLAUR domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 114.0), Kidney (RPKM 30.8) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q12

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (39874937..39922385, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (37326459..37368515, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (42219884..42263024, complement)

Chromosome 13 - NC_086031.1 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?

The 3' exon of the GPR39 gene overlaps with antisense gene LYPD1.
Title: GPR39 splice variants versus antisense gene LYPD1: expression and regulation in gastrointestinal tract, endocrine pancreas, liver, and white adipose tissue.

Submit: New GeneRIF Correction

General gene information

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Markers

D13Rat37 (e-PCR)
- UniSTS:118319

RH137955 (e-PCR)
- UniSTS:220042

D13Rat114 (e-PCR), detects polymorphism
- UniSTS:226510

AI853408 (e-PCR)
- UniSTS:165096

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables acetylcholine receptor binding	ISO Inferred from Sequence Orthology more info
enables acetylcholine receptor inhibitor activity	IBA Inferred from Biological aspect of Ancestor more info
enables acetylcholine receptor inhibitor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in acetylcholine receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within acetylcholine receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within behavioral fear response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of protein localization to plasma membrane	ISO Inferred from Sequence Orthology more info
acts_upstream_of protein localization to plasma membrane	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to nicotine	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within synaptic transmission, cholinergic	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in side of membrane	IEA Inferred from Electronic Annotation more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ly6/PLAUR domain-containing 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_001007727.1 → NP_001007728.1 ly6/PLAUR domain-containing protein 1 precursor

See identical proteins and their annotated locations for NP_001007728.1

Status: PROVISIONAL

Source sequence(s)

BC082032

UniProtKB/Swiss-Prot

Q66H42

UniProtKB/TrEMBL

A6K825

Related

ENSRNOP00000004741.3, ENSRNOT00000004741.6

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_086031.1 Reference GRCr8

Range

39874937..39922385 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063272438.1 → XP_063128508.1 ly6/PLAUR domain-containing protein 1 isoform X2
XM_017598845.3 → XP_017454334.1 ly6/PLAUR domain-containing protein 1 isoform X3
XM_063272437.1 → XP_063128507.1 ly6/PLAUR domain-containing protein 1 isoform X1