CCL16 C-C motif chemokine ligand 16 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCL16provided by HGNC
Official Full Name: C-C motif chemokine ligand 16provided by HGNC
Primary source: HGNC:HGNC:10614
See related: Ensembl:ENSG00000275152 MIM:601394; AllianceGenome:HGNC:10614
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LEC; LMC; NCC4; CKb12; HCC-4; LCC-1; Mtn-1; NCC-4; SCYL4; ILINCK; SCYA16
Summary: This gene is one of several cytokine genes clustered on the q-arm of chromosome 17. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for lymphocytes and monocytes but not for neutrophils. This cytokine also shows a potent myelosuppressive activity and suppresses proliferation of myeloid progenitor cells. The expression of this gene is upregulated by IL-10. [provided by RefSeq, Jul 2008]
Expression: Biased expression in liver (RPKM 21.1) and spleen (RPKM 0.6) See more
Orthologs: all
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Genomic context

Location:: 17q12

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (35976499..35981497, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (36924403..36931524, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (34303535..34308533, complement)

Chromosome 17 - NC_000017.11 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
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?

Characterizing ligand-receptor interactions and unveiling the pro-tumorigenic role of CCL16-CCR1 axis in the microenvironment of hepatocellular carcinoma.
Title: Characterizing ligand-receptor interactions and unveiling the pro-tumorigenic role of CCL16-CCR1 axis in the microenvironment of hepatocellular carcinoma.
Structure and Dynamics of Human Chemokine CCL16-Implications for Biological Activity.
Title: Structure and Dynamics of Human Chemokine CCL16-Implications for Biological Activity.
CC motif chemokine ligand 16 inhibits the progression of liver cirrhosis via inactivating hepatic stellate cells.
Title: CC motif chemokine ligand 16 inhibits the progression of liver cirrhosis via inactivating hepatic stellate cells.
CCL16 maintains stem cell-like properties in breast cancer by activating CCR2/GSK3beta/beta-catenin/OCT4 axis.
Title: CCL16 maintains stem cell-like properties in breast cancer by activating CCR2/GSK3β/β-catenin/OCT4 axis.
Single nucleotide polymorphism (SNPs) located in and around the C-C motif chemokine ligand 16 (CCL16) gene are associated with CCL16 protein levels in blood plasma, and rs80329614 is the SNP most strongly associated with CCL16 protein levels in plasma.
Title: Variants in CCL16 are associated with blood plasma and cerebrospinal fluid CCL16 protein levels.
High umbilical artery CCL16 is prominently detected in preterm preeclamptic pregnancies with severe growth restriction.
Title: Umbilical artery chemokine CCL16 is associated with preterm preeclampsia and fetal growth restriction.
Data show that CCL-16 gene expression was upregulated by 7.46-fold in IBS patients when compared with controls and suggest a subclinical inflammatory component underlying IBS.
Title: Pro-inflammatory chemokine C-C motif ligand 16 (CCL-16) dysregulation in irritable bowel syndrome (IBS): a pilot study.
Low umbilical cord blood chemokine CCL16 associates with spontaneous preterm birth
Title: Cord blood chemokines differentiate between spontaneous and elective preterm births in singleton pregnancies.
Elevated concentrations in bronchoalveolar lavage fluid from patients with eosinophilic pneumonia
Title: Elevated concentrations of liver-expressed chemokine/CC chemokine ligand 16 in bronchoalveolar lavage fluid from patients with eosinophilic pneumonia.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Genetic susceptibility to respiratory syncytial virus bronchiolitis in preterm children is associated with airway remodeling genes and innate immune genes.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

NoName (e-PCR)
- UniSTS:483887

D17S2005 (e-PCR)
- UniSTS:65074

D8S2279 (e-PCR)
- UniSTS:473907

D10S16 (e-PCR)
- UniSTS:155756

RH80030 (e-PCR)
- UniSTS:87680

D11S3114 (e-PCR)
- UniSTS:152207

L17971 (e-PCR)
- UniSTS:43966

RH98255 (e-PCR)
- UniSTS:88784

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables CCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables chemoattractant activity	IDA Inferred from Direct Assay more info	PubMed
enables chemokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell communication	TAS Traceable Author Statement more info	PubMed
involved_in cell-cell signaling	TAS Traceable Author Statement more info	PubMed
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemotaxis	TAS Traceable Author Statement more info	PubMed
involved_in eosinophil chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: C-C motif chemokine 16

Names: IL-10-inducible chemokine; chemokine (C-C motif) ligand 16; chemokine LEC; liver CC chemokine-1; liver-expressed chemokine; lymphocyte and monocyte chemoattractant; monotactin-1; new CC chemokine 4; small inducible cytokine subfamily A (Cys-Cys), member 16; small-inducible cytokine A16

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_004590.4 → NP_004581.1 C-C motif chemokine 16 precursor

See identical proteins and their annotated locations for NP_004581.1

Status: REVIEWED

Source sequence(s)

AB007454, AC244100, AF039955

Consensus CDS

CCDS11303.1

UniProtKB/Swiss-Prot

O15467, Q4KKU0

Related

ENSP00000478024.1, ENST00000611905.2

Conserved Domains (1) summary

cd00272
Location:37 → 92

Chemokine_CC; Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

35976499..35981497 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

211063..217475 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329312.1 → XP_054185287.1 C-C motif chemokine 16 isoform X1

UniProtKB/Swiss-Prot

O15467, Q4KKU0
XM_054329311.1 → XP_054185286.1 C-C motif chemokine 16 isoform X1

UniProtKB/Swiss-Prot

O15467, Q4KKU0

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

36924403..36931524 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054316871.1 → XP_054172846.1 C-C motif chemokine 16 isoform X1

UniProtKB/Swiss-Prot

O15467, Q4KKU0
XM_054316872.1 → XP_054172847.1 C-C motif chemokine 16 isoform X1

UniProtKB/Swiss-Prot

O15467, Q4KKU0