IL16 interleukin 16 [Homo sapiens (human)] - Gene

Summary

Official Symbol: IL16provided by HGNC
Official Full Name: interleukin 16provided by HGNC
Primary source: HGNC:HGNC:5980
See related: Ensembl:ENSG00000172349 MIM:603035
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: LCF; NIL16; PRIL16; prIL-16
Summary: The protein encoded by this gene is a pleiotropic cytokine that functions as a chemoattractant, a modulator of T cell activation, and an inhibitor of HIV replication. The signaling process of this cytokine is mediated by CD4. The product of this gene undergoes proteolytic processing, which is found to yield two functional proteins. The cytokine function is exclusively attributed to the secreted C-terminal peptide, while the N-terminal product may play a role in cell cycle control. Caspase 3 is reported to be involved in the proteolytic processing of this protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]
Expression: Broad expression in lymph node (RPKM 15.8), spleen (RPKM 12.1) and 20 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 15q25.1

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	15	NC_000015.10 (81196878..81312763)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (81474941..81605104)

Chromosome 15 - NC_000015.10 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
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 FunctionsWhat's a GeneRIF?

The present study demonstrated no association between IL-2 (T-330G), IL-16 (T-295C), and IL-17 (A-7383G) genotypes and CP in an Iranian population.
Title: Interleukin-2, -16, and -17 gene polymorphisms in Iranian patients with chronic periodontitis.
rs11556218 is associated with endometriosis in Greek women, probably by resulting in the aberrant expression of IL16
Title: The role of IL‑16 gene polymorphisms in endometriosis.
There was a decreased frequency of IL16 rs4778889 CC genotype carriers among women with gestational diabetes mellitus, however, there was no significant difference in the distribution of alleles.
Title: IL16 and IL18 gene polymorphisms in women with gestational diabetes.
Serum IL-6, serum YKL-40, and plasma VEGF were significantly correlated with disease activity at baseline in early rheumatoid arthritis.
Title: Circulating serum interleukin-6, serum chitinase-3-like protein-1, and plasma vascular endothelial growth factor are not predictive for remission and radiographic progression in patients with early rheumatoid arthritis: post-hoc explorative and validation studies based on the CIMESTRA and OPERA trials.
serum IL-16 level may not only serve as a useful diagnostic biomarker for patients with GC, but also may predict cancer recurrence and patient prognosis.
Title: Diagnostic and prognostic value of serum interleukin‑16 in patients with gastric cancer.
Association of interleukin 16 gene polymorphisms and plasma IL16 level with osteosarcoma risk.
Title: Association of interleukin 16 gene polymorphisms and plasma IL16 level with osteosarcoma risk.
Results suggest that IL16 genotype predict higher risk of death and progression, respectively, in NSCLC patients
Title: Interleukins as new prognostic genetic biomarkers in non-small cell lung cancer.
rs11556218 T/G genotype associated with increased risk for development of osteoporosis in Chinese postmenopausal women
Title: Interleukin-16 rs11556218 is associated with a risk of osteoporosis in Chinese postmenopausal women.
Data indicate an association between interleukin-16 (IL-16) rs4072111 and rs1131445 with progression to the severe stages (III-IV) of endometriosis.
Title: Association of interleukin-16 polymorphisms with disease progression and susceptibility in endometriosis.
Long-term exposure to tobacco smoke does not markedly alter extracellular concentrations of IL-16 protein in blood. However, it does decrease the intracellular IL-16 concentrations in blood NK cells.
Title: Interleukin-16-producing NK cells and T-cells in the blood of tobacco smokers with and without COPD.

Submit: New GeneRIF Correction See all GeneRIFs (106)

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

NHGRI GWAS Catalog

Description
Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations. NHGRI GWA Catalog NHGRI GWA 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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Replication interactions

Interaction	Pubs
Knockdown of interleukin 16 (IL16) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	IL-16 induces rapid translocation of PKC from the cytosol to the membrane in CD4+ cells; PKC inhibitors completely block IL-16-induced lymphocyte migration as well as the motile response induced by HIV-1 gp120 and anti-CD4 antibody binding to CD4	PubMed
Tat	tat	Recombinant IL-16 inhibits HIV-1 Tat activation of the HIV-1 LTR promoter	PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

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Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
Immune System, organism-specific biosystem (from REACTOME)
Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
Signaling by Interleukins, organism-specific biosystem (from REACTOME)
Signaling by Interleukins, organism-specific biosystemInterleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but a...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-H57532 (e-PCR)
- UniSTS:51215

G59841 (e-PCR)
- UniSTS:136990

RH69578 (e-PCR)
- UniSTS:41787

WI-11334 (e-PCR)
- UniSTS:21330

RH120871 (e-PCR)
- UniSTS:32365

IL16_753 (e-PCR)
- UniSTS:277365

STS-W15415 (e-PCR)
- UniSTS:38295

SHGC-12749 (e-PCR)
- UniSTS:66458

SHGC-83106 (e-PCR)
- UniSTS:101332

PMC15509P1 (e-PCR)
- UniSTS:271326

Homology

Homologs of the IL16 gene: The IL16 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, and frog.
Orthologs from Annotation Pipeline: 242 organisms have orthologs with human gene IL16
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
CD4 receptor binding	IPI Inferred from Physical Interaction more info	PubMed
cytokine activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
cytokine-mediated signaling pathway	TAS Traceable Author Statement more info
immune response	TAS Traceable Author Statement more info	PubMed
induction of positive chemotaxis	IEA Inferred from Electronic Annotation more info
leukocyte chemotaxis	IEA Inferred from Electronic Annotation more info
regulation of calcium ion transport	IDA Inferred from Direct Assay more info	PubMed
regulation of signaling receptor activity	IEA Inferred from Electronic Annotation more info
viral process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cytosol	IDA Inferred from Direct Assay more info
cytosol	TAS Traceable Author Statement more info
extracellular region	TAS Traceable Author Statement more info
extracellular space	IEA Inferred from Electronic Annotation more info
nuclear speck	IDA Inferred from Direct Assay more info
plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: pro-interleukin-16

Names: lymphocyte chemoattractant factor; neuronal interleukin 16; prointerleukin 16

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.

Genomic

NG_029933.1 RefSeqGene

Range

5001..120886

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001172128.1 → NP_001165599.1 pro-interleukin-16 isoform 3

See identical proteins and their annotated locations for NP_001165599.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is longer, compared to isoform 1.

Source sequence(s)

AC103858, AK124725, AK131530

Consensus CDS

CCDS53966.1

UniProtKB/Swiss-Prot

Q14005

Related

ENSP00000378155.2, ENST00000394660.6

Conserved Domains (2) summary

smart00228
Location:1233 → 1319

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:217 → 300

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
NM_001352684.1 → NP_001339613.1 pro-interleukin-16 isoform 4

Status: REVIEWED

Source sequence(s)

AC036196, AC103858, AY324389

Conserved Domains (3) summary

smart00228
Location:624 → 710

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:501 → 578

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cl27818
Location:250 → 345

COG1615; Uncharacterized membrane protein, UPF0182 family [Function unknown]
NM_001352685.1 → NP_001339614.1 pro-interleukin-16 isoform 5

Status: REVIEWED

Source sequence(s)

AC036196, AC103858, AY324389

Conserved Domains (3) summary

smart00228
Location:1063 → 1149

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:47 → 130

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cl27818
Location:690 → 785

COG1615; Uncharacterized membrane protein, UPF0182 family [Function unknown]
NM_001352686.1 → NP_001339615.1 pro-interleukin-16 isoform 6

Status: REVIEWED

Source sequence(s)

AC036196, AC103858, AY324389

Conserved Domains (3) summary

smart00228
Location:1284 → 1370

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:268 → 351

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cl27818
Location:911 → 1006

COG1615; Uncharacterized membrane protein, UPF0182 family [Function unknown]
NM_004513.5 → NP_004504.3 pro-interleukin-16 isoform 1

See identical proteins and their annotated locations for NP_004504.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform (1).

Source sequence(s)

AC103858, DB141707, U82972

Consensus CDS

CCDS10317.1

UniProtKB/Swiss-Prot

Q14005

UniProtKB/TrEMBL

Q9UME6

Related

ENSP00000378147.2, ENST00000394652.6

Conserved Domains (3) summary

smart00228
Location:533 → 619

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:410 → 487

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cl23717
Location:347 → 432

crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
NM_172217.4 → NP_757366.2 pro-interleukin-16 isoform 2

See identical proteins and their annotated locations for NP_757366.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is longer at the N-terminus compared to isoform 1.

Source sequence(s)

AC036196, AC103858, AY324389

Consensus CDS

CCDS42069.1

UniProtKB/Swiss-Prot

Q14005

Related

ENSP00000302935.4, ENST00000302987.8

Conserved Domains (2) summary

smart00228
Location:1234 → 1320

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:217 → 300

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...