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Lyn LYN proto-oncogene, Src family tyrosine kinase [ Rattus norvegicus (Norway rat) ]

Gene ID: 81515, updated on 2-May-2024

Summary

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Official Symbol: Lynprovided by RGD
Official Full Name: LYN proto-oncogene, Src family tyrosine kinaseprovided by RGD
Primary source: RGD:621017
See related: Ensembl:ENSRNOG00000008180 AllianceGenome:RGD:621017
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: p53Lyn; p56Lyn
Summary: Enables several functions, including gamma-tubulin binding activity; signaling receptor binding activity; and ubiquitin protein ligase binding activity. Involved in several processes, including histamine secretion by mast cell; neurogenesis; and positive regulation of Fc receptor mediated stimulatory signaling pathway. Located in several cellular components, including adherens junction; mitochondrial envelope; and postsynaptic density. Part of integrin alpha2-beta1 complex. Is active in glutamatergic synapse and postsynaptic specialization, intracellular component. Biomarker of Parkinsonism and endometriosis. Orthologous to human LYN (LYN proto-oncogene, Src family tyrosine kinase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 493.9), Lung (RPKM 314.9) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

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See Lyn in Genome Data Viewer

Location:: 5q12

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (21437127..21553097)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (16639512..16755501)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (16526058..16642648)

Chromosome 5 - NC_086023.1 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?

This study reveals a complex regulation for PLSCR1 tyrosine phosphorylation in FcepsilonRI-activated mast cells, and that PLSCR1 sits at a crossroads between Lyn and Fyn pathways.
Title: Regulation of the tyrosine phosphorylation of Phospholipid Scramblase 1 in mast cells that are stimulated through the high-affinity IgE receptor.
Mitochondrial tyrosine phosphorylation, negligible in the quiescent liver, was detected in the early phases of liver regeneration with a trend similar to the events heralding mitochondrial apoptosis and was attributed to the tyrosine kinase Lyn
Title: Lyn-mediated mitochondrial tyrosine phosphorylation is required to preserve mitochondrial integrity in early liver regeneration.
Integrin-associated Lyn kinase acts as a key upstream kinase that may play a critical role in cerebral ischemia/reperfusion injury
Title: Integrin-associated Lyn kinase promotes cell survival by suppressing acid sphingomyelinase activity.
PLSCR1 is a novel amplifier of FcepsilonRI signaling that acts selectively on the Lyn-initiated LAT/phospholipase Cgamma1/calcium axis, resulting in potentiation of a selected set of mast cell responses
Title: Phospholipid scramblase 1 modulates a selected set of IgE receptor-mediated mast cell responses through LAT-dependent pathway.
Lyn is a novel regulator of phagocytosis by alveolar macrophages during Pseudomonas infection.
Title: Cholesterol-rich membrane rafts and Lyn are involved in phagocytosis during Pseudomonas aeruginosa infection.
TOM1L1 is a novel protein involved in the FcepsilonRI signal transduction for the generation of cytokines that acts as a Lyn substrate
Title: TOM1L1 is a Lyn substrate involved in FcepsilonRI signaling in mast cells.
Lyn may be a critical kinase mediating nerve injury-induced P2X(4)R upregulation and neuropathic pain
Title: Lyn tyrosine kinase is required for P2X(4) receptor upregulation and neuropathic pain after peripheral nerve injury.
Lyn is present in pancreatic acinar cells and is involved in the cellular signaling by gastrointestinal growth factors and hormones/neurotransmitters that are known to alter pancreatic acinar cell function.
Title: The Src family kinase, Lyn, is activated in pancreatic acinar cells by gastrointestinal hormones/neurotransmitters and growth factors which stimulate its association with numerous other signaling molecules.
Lipid rafts segregate activated components of signalling pathways into membrane microdomains where they are in close juxtaposition. The Lyn protein in lipid rafts was tyrosine-phosphorylated (activated)in accordance with this proposed microdomain role.
Title: Isolation and characterization of lipid rafts with different properties from RBL-2H3 (rat basophilic leukaemia) cells.
Lyn recovered from lipid rafts has a substantially higher specific activity than Lyn from nonraft environments.
Title: A lipid raft environment enhances Lyn kinase activity by protecting the active site tyrosine from dephosphorylation.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH94837 (e-PCR)
- UniSTS:120083

RH94838 (e-PCR)
- UniSTS:120084

AU027765 (e-PCR)
- UniSTS:112987

RH140554 (e-PCR)
- UniSTS:222623

D5Rat206 (e-PCR)
- UniSTS:240351

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables SH3 domain binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables ephrin receptor binding	ISO Inferred from Sequence Orthology more info
enables gamma-tubulin binding	IDA Inferred from Direct Assay more info	PubMed
enables glycosphingolipid binding	IPI Inferred from Physical Interaction more info	PubMed
enables integrin binding	IDA Inferred from Direct Assay more info	PubMed
enables kinase activity	TAS Traceable Author Statement more info	PubMed
enables non-membrane spanning protein tyrosine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables non-membrane spanning protein tyrosine kinase activity	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol 3-kinase activator activity	ISO Inferred from Sequence Orthology more info
enables phosphoprotein binding	IPI Inferred from Physical Interaction more info	PubMed
enables phosphorylation-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables platelet-derived growth factor receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activity	ISO Inferred from Sequence Orthology more info
enables protein tyrosine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein tyrosine kinase activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables scaffold protein binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane transporter binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in B cell homeostasis	ISO Inferred from Sequence Orthology more info
involved_in B cell homeostasis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within B cell receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in C-X-C chemokine receptor CXCR4 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in DNA damage checkpoint signaling	IEA Inferred from Electronic Annotation more info
involved_in DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in DNA damage response	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in Fc receptor mediated inhibitory signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in Fc receptor mediated inhibitory signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in Fc receptor mediated stimulatory signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in Fc receptor mediated stimulatory signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in Fc receptor mediated stimulatory signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in cell surface receptor protein tyrosine kinase signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell surface receptor protein tyrosine kinase signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cellular response to heat	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to retinoic acid	ISO Inferred from Sequence Orthology more info
involved_in dendritic cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in dendritic cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in dendritic cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in eosinophil differentiation	ISO Inferred from Sequence Orthology more info
involved_in erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in erythrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in fatty acid transport	ISO Inferred from Sequence Orthology more info
involved_in hematopoietic progenitor cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in hemopoiesis	ISO Inferred from Sequence Orthology more info
involved_in histamine secretion by mast cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in immune response-regulating cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in immune response-regulating cell surface receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in interleukin-5-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within intracellular signal transduction	ISO Inferred from Sequence Orthology more info
involved_in lipopolysaccharide-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in lipopolysaccharide-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of B cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of ERK1 and ERK2 cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of intracellular signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of intracellular signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of mast cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mast cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of myeloid leukocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of toll-like receptor 2 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of toll-like receptor 2 signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of toll-like receptor 4 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of toll-like receptor 4 signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron projection development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in oligodendrocyte development	IEP Inferred from Expression Pattern more info	PubMed
involved_in platelet degranulation	ISO Inferred from Sequence Orthology more info
involved_in platelet degranulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of Fc receptor mediated stimulatory signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of MAPK cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of MAPK cascade	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of dendritic cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dendritic cell apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of glial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mast cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of oligodendrocyte progenitor proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tyrosine phosphorylation of STAT protein	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tyrosine phosphorylation of STAT protein	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein phosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of B cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of B cell receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of B cell receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of B cell receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in regulation of ERK1 and ERK2 cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell adhesion mediated by integrin	ISO Inferred from Sequence Orthology more info
involved_in regulation of cytokine production	ISO Inferred from Sequence Orthology more info
involved_in regulation of cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of erythrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in regulation of mast cell activation	ISO Inferred from Sequence Orthology more info
involved_in regulation of mast cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mast cell degranulation	ISO Inferred from Sequence Orthology more info
involved_in regulation of mast cell degranulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of monocyte chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in regulation of platelet aggregation	ISO Inferred from Sequence Orthology more info
involved_in regulation of platelet aggregation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of release of sequestered calcium ion into cytosol	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of release of sequestered calcium ion into cytosol	ISO Inferred from Sequence Orthology more info
involved_in response to amino acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to axon injury	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to carbohydrate	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to hormone	ISO Inferred from Sequence Orthology more info
involved_in response to hormone	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to insulin	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to peptide hormone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to sterol depletion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to toxic substance	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in tolerance induction to self antigen	IBA Inferred from Biological aspect of Ancestor more info
involved_in tolerance induction to self antigen	ISO Inferred from Sequence Orthology more info
involved_in tolerance induction to self antigen	ISS Inferred from Sequence or Structural Similarity more info
involved_in toll-like receptor 4 signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in adherens junction	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasmic side of plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
part_of integrin alpha2-beta1 complex	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in mitochondrial crista	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic specialization, intracellular component	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: tyrosine-protein kinase Lyn

Names: Yamaguchi sarcoma viral (v-yes-1) oncogene homolog; lyn protein non-receptor kinase; v-yes-1 Yamaguchi sarcoma viral related oncogene homolog

NP_001104568.1

EC 2.7.10.2

NP_110484.1

EC 2.7.10.2

XP_006237896.1

EC 2.7.10.2

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_001111098.1 → NP_001104568.1 tyrosine-protein kinase Lyn isoform B

See identical proteins and their annotated locations for NP_001104568.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform B).

Source sequence(s)

AF000301, JAXUCZ010000005

UniProtKB/TrEMBL

A6JFK9

Conserved Domains (4) summary

cd10364
Location:104 → 204

SH2_Src_Lyn; Src homology 2 (SH2) domain found in Lyn

cd12004
Location:46 → 101

SH3_Lyn; Src homology 3 domain of Lyn Protein Tyrosine Kinase

cd05072
Location:218 → 489

PTKc_Lyn; Catalytic domain of the Protein Tyrosine Kinase, Lyn

pfam07714
Location:226 → 476

Pkinase_Tyr; Protein tyrosine kinase
NM_030857.2 → NP_110484.1 tyrosine-protein kinase Lyn isoform A

See identical proteins and their annotated locations for NP_110484.1

Status: VALIDATED

Description

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

Source sequence(s)

AF000300, AF000301, JAXUCZ010000005

UniProtKB/Swiss-Prot

Q07014, Q63320

UniProtKB/TrEMBL

A6JFK8

Related

ENSRNOP00000011130.4, ENSRNOT00000011130.6

Conserved Domains (4) summary

cd10364
Location:125 → 225

SH2_Src_Lyn; Src homology 2 (SH2) domain found in Lyn

cd12004
Location:67 → 122

SH3_Lyn; Src homology 3 domain of Lyn Protein Tyrosine Kinase

cd05072
Location:239 → 510

PTKc_Lyn; Catalytic domain of the Protein Tyrosine Kinase, Lyn

pfam07714
Location:247 → 497

Pkinase_Tyr; Protein tyrosine kinase

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_086023.1 Reference GRCr8

Range

21437127..21553097

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006237834.5 → XP_006237896.1 tyrosine-protein kinase Lyn isoform X1

See identical proteins and their annotated locations for XP_006237896.1

UniProtKB/Swiss-Prot

Q07014, Q63320

UniProtKB/TrEMBL

A6JFK8

Conserved Domains (4) summary

cd10364
Location:125 → 225

SH2_Src_Lyn; Src homology 2 (SH2) domain found in Lyn

cd12004
Location:67 → 122

SH3_Lyn; Src homology 3 domain of Lyn Protein Tyrosine Kinase

cd05072
Location:239 → 510

PTKc_Lyn; Catalytic domain of the Protein Tyrosine Kinase, Lyn

pfam07714
Location:247 → 497

Pkinase_Tyr; Protein tyrosine kinase