CHID1 chitinase domain containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHID1provided by HGNC
Official Full Name: chitinase domain containing 1provided by HGNC
Primary source: HGNC:HGNC:28474
See related: Ensembl:ENSG00000177830 MIM:615692; AllianceGenome:HGNC:28474
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GL008; SICLP; SI-CLP
Summary: Enables oligosaccharide binding activity. Involved in negative regulation of cytokine production involved in inflammatory response. Located in several cellular components, including late endosome; lysosome; and trans-Golgi network. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Ubiquitous expression in testis (RPKM 12.9), spleen (RPKM 11.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p15.5

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (867859..915214, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (919274..966273, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (867859..914845, complement)

Chromosome 11 - NC_000011.10 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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Chitinase domain containing 1 increase is associated with low survival rate and M0 macrophages infiltrates in colorectal cancer patients.
Title: Chitinase domain containing 1 increase is associated with low survival rate and M0 macrophages infiltrates in colorectal cancer patients.
Brain CHID1 Expression Correlates with NRGN and CALB1 in Healthy Subjects and AD Patients.
Title: Brain CHID1 Expression Correlates with NRGN and CALB1 in Healthy Subjects and AD Patients.
CHID1 Is a Novel Prognostic Marker of Non-Small Cell Lung Cancer.
Title: CHID1 Is a Novel Prognostic Marker of Non-Small Cell Lung Cancer.
These results indicate that CHID1 positively regulates RLR antiviral signal, revealing the novel mechanism of the RIG-I antiviral signaling pathway.
Title: CHID1 positively regulates RLR antiviral signaling by targeting the RIG-I/VISA signalosome.
This review comprehensively analyzes recent data about expression pattern, and involvement of human YKL-40, YKL-39 and SI-CLP in cancer. [review]
Title: Role of chitinase-like proteins in cancer.
stabilin-1-interacting chitinase-like protein functions as a regulator of the inflammatory response in rheumatoid arthritis by macrophages.
Title: Human secreted stabilin-1-interacting chitinase-like protein aggravates the inflammation associated with rheumatoid arthritis and is a potential macrophage inflammatory regulator in rodents.
Structure of human stabilin-1 interacting chitinase-like protein (SI-CLP) reveals a saccharide-binding cleft with lower sugar-binding selectivity.
Title: Structure of human stabilin-1 interacting chitinase-like protein (SI-CLP) reveals a saccharide-binding cleft with lower sugar-binding selectivity.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
The crystals of SI-CLP belong to the space group P3(2)21 with unit cell parameters a=b=99.79 A, c=250.53 A, alpha=beta=90 degrees, gamma=120 degrees.
Title: Crystallization and preliminary X-ray crystallographic studies on SI-CLP, a novel human Glyco_18 domain-containing protein.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic susceptibility for chronic bronchitis in chronic obstructive pulmonary disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp160, precursor	env	HIV-1 gp160 interacts with CHID1; predicted interaction to be relevant to viral egress at plasma membrane/extracellular matrix	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH47630 (e-PCR)
- UniSTS:29718

RH69933 (e-PCR)
- UniSTS:78643

D8S2279 (e-PCR)
- UniSTS:473907

RH65976 (e-PCR)
- UniSTS:63825

RH12084 (e-PCR)
- UniSTS:11095

WI-18565 (e-PCR)
- UniSTS:53100

SHGC-148169 (e-PCR)
- UniSTS:176238

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chitin binding	IEA Inferred from Electronic Annotation more info
enables oligosaccharide binding	IBA Inferred from Biological aspect of Ancestor more info
enables oligosaccharide binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in carbohydrate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cytokine production involved in inflammatory response	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal lumen	TAS Traceable Author Statement more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: chitinase domain-containing protein 1

Names: stabilin-1 interacting chitinase-like protein

NP_001136146.1

EC 3.6.5.4

NP_001136147.1

EC 3.6.5.4

NP_001136148.1

EC 3.6.5.4

NP_001136149.1

EC 3.6.5.4

NP_076436.3

EC 3.6.5.4

XP_011518601.1

EC 3.6.5.4

XP_011518602.1

EC 3.6.5.4

XP_011518603.1

EC 3.6.5.4

XP_011518604.1

EC 3.6.5.4

XP_016873655.1

EC 3.6.5.4

XP_016873656.1

EC 3.6.5.4

XP_024304431.1

EC 3.6.5.4

XP_047283435.1

EC 3.6.5.4

XP_047283436.1

EC 3.6.5.4

XP_047283437.1

EC 3.6.5.4

XP_047283438.1

EC 3.6.5.4

XP_047283439.1

EC 3.6.5.4

XP_047283440.1

EC 3.6.5.4

XP_047283441.1

EC 3.6.5.4

XP_047283442.1

EC 3.6.5.4

XP_054225699.1

EC 3.6.5.4

XP_054225700.1

EC 3.6.5.4

XP_054225701.1

EC 3.6.5.4

XP_054225702.1

EC 3.6.5.4

XP_054225703.1

EC 3.6.5.4

XP_054225704.1

EC 3.6.5.4

XP_054225705.1

EC 3.6.5.4

XP_054225706.1

EC 3.6.5.4

XP_054225707.1

EC 3.6.5.4

XP_054225708.1

EC 3.6.5.4

XP_054225709.1

EC 3.6.5.4

XP_054225710.1

EC 3.6.5.4

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_001142674.2 → NP_001136146.1 chitinase domain-containing protein 1 isoform a precursor

See identical proteins and their annotated locations for NP_001136146.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode isoform a.

Source sequence(s)

AP006623, BC000001, BI818660, CK904484

Consensus CDS

CCDS7722.1

UniProtKB/Swiss-Prot

B3KWB0, Q8NBM9, Q96CZ3, Q96S93, Q96SK0, Q9BWS9, Q9BY52

UniProtKB/TrEMBL

B7Z705

Related

ENSP00000388156.2, ENST00000436108.6

Conserved Domains (1) summary

cd02876
Location:77 → 393

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...
NM_001142675.2 → NP_001136147.1 chitinase domain-containing protein 1 isoform a precursor

See identical proteins and their annotated locations for NP_001136147.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode isoform a.

Source sequence(s)

AP006623, BC095409, BI821281, CK904484, DA983719

Consensus CDS

CCDS7722.1

UniProtKB/Swiss-Prot

B3KWB0, Q8NBM9, Q96CZ3, Q96S93, Q96SK0, Q9BWS9, Q9BY52

UniProtKB/TrEMBL

B7Z705

Related

ENSP00000391255.1, ENST00000449825.5

Conserved Domains (1) summary

cd02876
Location:77 → 393

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...
NM_001142676.2 → NP_001136148.1 chitinase domain-containing protein 1 isoform b precursor

See identical proteins and their annotated locations for NP_001136148.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and contains an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (b) has the same N- and C-termini but includes an additional segment, compared to isoform a.

Source sequence(s)

AK075413, AP006623, CK904484

Consensus CDS

CCDS44511.1

UniProtKB/TrEMBL

B7Z705

Related

ENSP00000435503.1, ENST00000528581.5

Conserved Domains (2) summary

cd02876
Location:102 → 418

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...

smart00636
Location:106 → 409

Glyco_18; Glyco_18 domain
NM_001142677.2 → NP_001136149.1 chitinase domain-containing protein 1 isoform c precursor

See identical proteins and their annotated locations for NP_001136149.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon in the central coding region, compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter than isoform a.

Source sequence(s)

AP006623, AY037151, CK904484

Consensus CDS

CCDS44510.1

UniProtKB/TrEMBL

B7Z705

Related

ENSP00000416034.2, ENST00000429789.6

Conserved Domains (2) summary

cd02876
Location:77 → 362

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...

smart00636
Location:81 → 353

Glyco_18; Glyco_18 domain
NM_023947.4 → NP_076436.3 chitinase domain-containing protein 1 isoform a precursor

See identical proteins and their annotated locations for NP_076436.3

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode isoform a.

Source sequence(s)

AP006623, BC095409, CK904484

Consensus CDS

CCDS7722.1

UniProtKB/Swiss-Prot

B3KWB0, Q8NBM9, Q96CZ3, Q96S93, Q96SK0, Q9BWS9, Q9BY52

UniProtKB/TrEMBL

B7Z705

Related

ENSP00000325055.8, ENST00000323578.13

Conserved Domains (1) summary

cd02876
Location:77 → 393

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

867859..915214 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011520300.3 → XP_011518602.1 chitinase domain-containing protein 1 isoform X2

UniProtKB/TrEMBL

B7Z705

Conserved Domains (2) summary

cd02876
Location:162 → 447

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...

smart00636
Location:166 → 438

Glyco_18; Glyco_18 domain
XM_011520299.3 → XP_011518601.1 chitinase domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

B7Z705

Conserved Domains (2) summary

cd02876
Location:162 → 478

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...

smart00636
Location:166 → 469

Glyco_18; Glyco_18 domain
XM_047427479.1 → XP_047283435.1 chitinase domain-containing protein 1 isoform X5

UniProtKB/Swiss-Prot

B3KWB0, Q8NBM9, Q96CZ3, Q96S93, Q96SK0, Q9BWS9, Q9BY52
XM_047427480.1 → XP_047283436.1 chitinase domain-containing protein 1 isoform X5

UniProtKB/Swiss-Prot

B3KWB0, Q8NBM9, Q96CZ3, Q96S93, Q96SK0, Q9BWS9, Q9BY52
XM_047427484.1 → XP_047283440.1 chitinase domain-containing protein 1 isoform X8
XM_047427481.1 → XP_047283437.1 chitinase domain-containing protein 1 isoform X5

UniProtKB/Swiss-Prot

B3KWB0, Q8NBM9, Q96CZ3, Q96S93, Q96SK0, Q9BWS9, Q9BY52
XM_017018166.2 → XP_016873655.1 chitinase domain-containing protein 1 isoform X5

UniProtKB/Swiss-Prot

B3KWB0, Q8NBM9, Q96CZ3, Q96S93, Q96SK0, Q9BWS9, Q9BY52

UniProtKB/TrEMBL

B7Z705

Conserved Domains (1) summary

cd02876
Location:77 → 393

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...
XM_011520301.4 → XP_011518603.1 chitinase domain-containing protein 1 isoform X3

Conserved Domains (2) summary

cd02876
Location:162 → 405

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...

smart00636
Location:166 → 397

Glyco_18; Glyco_18 domain
XM_047427485.1 → XP_047283441.1 chitinase domain-containing protein 1 isoform X9
XM_024448663.2 → XP_024304431.1 chitinase domain-containing protein 1 isoform X7

Conserved Domains (1) summary

cd02876
Location:77 → 320

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...
XM_047427482.1 → XP_047283438.1 chitinase domain-containing protein 1 isoform X6
XM_011520302.4 → XP_011518604.1 chitinase domain-containing protein 1 isoform X4

Conserved Domains (2) summary

cd02876
Location:162 → 404

GH18_SI-CLP; Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl ...

smart00636
Location:166 → 397

Glyco_18; Glyco_18 domain
XM_047427483.1 → XP_047283439.1 chitinase domain-containing protein 1 isoform X10
XM_047427486.1 → XP_047283442.1 chitinase domain-containing protein 1 isoform X11
XM_017018167.3 → XP_016873656.1 chitinase domain-containing protein 1 isoform X10

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

919274..966273 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054369731.1 → XP_054225706.1 chitinase domain-containing protein 1 isoform X8
XM_054369728.1 → XP_054225703.1 chitinase domain-containing protein 1 isoform X5
XM_054369725.1 → XP_054225700.1 chitinase domain-containing protein 1 isoform X2
XM_054369724.1 → XP_054225699.1 chitinase domain-containing protein 1 isoform X1
XM_054369726.1 → XP_054225701.1 chitinase domain-containing protein 1 isoform X3
XM_054369732.1 → XP_054225707.1 chitinase domain-containing protein 1 isoform X9
XM_054369730.1 → XP_054225705.1 chitinase domain-containing protein 1 isoform X7
XM_054369734.1 → XP_054225709.1 chitinase domain-containing protein 1 isoform X10
XM_054369729.1 → XP_054225704.1 chitinase domain-containing protein 1 isoform X6
XM_054369727.1 → XP_054225702.1 chitinase domain-containing protein 1 isoform X4
XM_054369735.1 → XP_054225710.1 chitinase domain-containing protein 1 isoform X11
XM_054369733.1 → XP_054225708.1 chitinase domain-containing protein 1 isoform X10