Chi3l1 chitinase 3 like 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Chi3l1provided by RGD
Official Full Name: chitinase 3 like 1provided by RGD
Primary source: RGD:620874
See related: EnsemblRapid:ENSRNOG00000053272 AllianceGenome:RGD:620874
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: Chil1; GP-39; YKL40; CGP-39; YKL-40
Summary: Predicted to enable chitin binding activity. Involved in cellular response to interleukin-1; cellular response to tumor necrosis factor; and inflammatory response. Located in extracellular space. Biomarker of hypertension. Human ortholog(s) of this gene implicated in asthma and schizophrenia. Orthologous to human CHI3L1 (chitinase 3 like 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 301.3), Spleen (RPKM 122.9) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q13

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (48193839..48201822)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (45641802..45649787)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (51022844..51030797)

Chromosome 13 - NC_086031.1 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?

YKL-40 Knockdown Decreases Oxidative Stress Damage in Ovarian Granulosa Cells.
Title: YKL-40 Knockdown Decreases Oxidative Stress Damage in Ovarian Granulosa Cells.
M2a Macrophage-Secreted CHI3L1 Promotes Extracellular Matrix Metabolic Imbalances via Activation of IL-13Ralpha2/MAPK Pathway in Rat Intervertebral Disc Degeneration.
Title: M2a Macrophage-Secreted CHI3L1 Promotes Extracellular Matrix Metabolic Imbalances via Activation of IL-13Rα2/MAPK Pathway in Rat Intervertebral Disc Degeneration.
Effects of chitinase-3-like protein 1 on brain death-induced hepatocyte apoptosis via PAR2-JNK-caspase-3.
Title: Effects of chitinase-3-like protein 1 on brain death-induced hepatocyte apoptosis via PAR2-JNK-caspase-3.
Astrocytes induce proliferation of oligodendrocyte progenitor cells via connexin 47-mediated activation of Chi3l1 expression.
Title: Astrocytes induce proliferation of oligodendrocyte progenitor cells via connexin 47-mediated activation of Chi3l1 expression.
the data indicated that miR30a5p promoted cell growth and inhibited apoptosis of human pulmonary artery endothelial cells under hypoxia by targeting YKL40. Therefore, the miR30a5p/YKL40 axis may provide a potential target for the development of novel Pulmonary arterial hypertension (PAH) therapies.
Title: MicroRNA‑30a‑5p promotes proliferation and inhibits apoptosis of human pulmonary artery endothelial cells under hypoxia by targeting YKL‑40.
Results showed that protein and mRNA levels of CHI3L1 decreased in normal cartilage but increased in osteoarthritic cartilage.
Title: Co-Expression and Co-Localization of Cartilage Glycoproteins CHI3L1 and Lubricin in Osteoarthritic Cartilage: Morphological, Immunohistochemical and Gene Expression Profiles.
NGF-treated tissue showed increased expression of CHI3L1 which was inhibited by the presence of Ro 08-2750 in intervertebral disk cells.
Title: Nerve growth factor promotes expression of novel genes in intervertebral disc cells that regulate tissue degradation: Laboratory investigation.
I/R injury in steatotic livers resulted in significant increases in expression of YKL-40 (9 fold), and activation of MMP-2 (15 fold)/MMP-9 (12 fold).
Title: Protective role of bortezomib in steatotic liver ischemia/reperfusion injury through abrogation of MMP activation and YKL-40 expression.
Data show that hepatic CD14+ cells are an YKL-40(Chi3L1)mRNA and protein source in acute and chronic liver injury, with expression patterns similar to growth factors implicated in inflammation-fibrogenesis
Title: YKL-40 expression in CD14⁺ liver cells in acute and chronic injury.
induction and continued secretion of CHI3L1 in chondrocytes require sustained activation of NF-kappaB
Title: Inflammatory cytokines induce production of CHI3L1 by articular chondrocytes.

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General gene information

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Markers

BE106626 (e-PCR)
- UniSTS:246340

RH142356 (e-PCR)
- UniSTS:231603

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables chitin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chitin binding	IEA Inferred from Electronic Annotation more info
enables chitin binding	ISO Inferred from Sequence Orthology more info
enables chitin binding	ISS Inferred from Sequence or Structural Similarity more info
NOT enables chitinase activity	IBA Inferred from Biological aspect of Ancestor more info
NOT enables chitinase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in activation of NF-kappaB-inducing kinase activity	ISO Inferred from Sequence Orthology more info
involved_in activation of NF-kappaB-inducing kinase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in carbohydrate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in cellular response to interleukin-1	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to tumor necrosis factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in chitin catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEP Inferred from Expression Pattern more info	PubMed
involved_in inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in lung development	IEA Inferred from Electronic Annotation more info
involved_in lung development	ISO Inferred from Sequence Orthology more info
involved_in lung development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of ERK1 and ERK2 cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ERK1 and ERK2 cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-8 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-8 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of peptidyl-threonine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of peptidyl-threonine phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to interleukin-1	IEA Inferred from Electronic Annotation more info
involved_in response to interleukin-1	ISO Inferred from Sequence Orthology more info
involved_in response to interleukin-1	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to interleukin-6	IEA Inferred from Electronic Annotation more info
involved_in response to interleukin-6	ISO Inferred from Sequence Orthology more info
involved_in response to interleukin-6	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to mechanical stimulus	IEA Inferred from Electronic Annotation more info
involved_in response to mechanical stimulus	ISO Inferred from Sequence Orthology more info
involved_in response to mechanical stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to tumor necrosis factor	IEA Inferred from Electronic Annotation more info
involved_in response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
involved_in response to tumor necrosis factor	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
is_active_in extracellular region	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	IEA Inferred from Electronic Annotation more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chitinase-3-like protein 1

Names: cartilage glycoprotein 39; chitinase 3-like 1 (cartilage glycoprotein-39); chitinase 3-like 1 protein

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_001309820.1 → NP_001296749.1 chitinase-3-like protein 1 isoform 1 precursor

See identical proteins and their annotated locations for NP_001296749.1

Status: VALIDATED

Description

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

Source sequence(s)

BC091365, JAXUCZ010000013

UniProtKB/TrEMBL

A0A8I6AFN7, A6ICA7, A6ICA8

Related

ENSRNOP00000091690.1, ENSRNOT00000108902.2

Conserved Domains (2) summary

cd02872
Location:32 → 388

GH18_chitolectin_chitotriosidase; This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active ...

smart00636
Location:31 → 365

Glyco_18; Glyco_18 domain
NM_053560.2 → NP_446012.2 chitinase-3-like protein 1 isoform 2 precursor

See identical proteins and their annotated locations for NP_446012.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' structure compared to variant 1. The encoded isoform (2) has a distinct N-terminus, and is shorter than isoform 1.

Source sequence(s)

BC091365, JAXUCZ010000013

UniProtKB/Swiss-Prot

Q5BJR6, Q9WTV1

UniProtKB/TrEMBL

A6ICA6, A6ICA8

Related

ENSRNOP00000074871.1, ENSRNOT00000078599.3

Conserved Domains (2) summary

cd02872
Location:22 → 378

GH18_chitolectin_chitotriosidase; This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active ...

smart00636
Location:21 → 355

Glyco_18; Glyco_18 domain