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    IL16 interleukin 16 [ Homo sapiens (human) ]

    Gene ID: 3603, updated on 27-Nov-2024

    Summary

    Official Symbol
    IL16provided by HGNC
    Official Full Name
    interleukin 16provided by HGNC
    Primary source
    HGNC:HGNC:5980
    See related
    Ensembl:ENSG00000172349 MIM:603035; AllianceGenome:HGNC:5980
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See IL16 in Genome Data Viewer
    Location:
    15q25.1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (81182712..81314058)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (79045899..79178128)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (81489220..81606399)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9948 Neighboring gene cilia and flagella associated protein 161 Neighboring gene acidic nuclear phosphoprotein 32 family member B pseudogene 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:81481874-81483073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9949 Neighboring gene Sharpr-MPRA regulatory regions 3481 and 15421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9951 Neighboring gene NANOG hESC enhancer GRCh37_chr15:81585795-81586313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:81588972-81589538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:81589539-81590103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9956 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:81595578-81596777 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:81600895-81601072 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:81605226-81606425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6743 Neighboring gene TMC3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:81648807-81649306 Neighboring gene StAR related lipid transfer domain containing 5 Neighboring gene transmembrane channel like 3 Neighboring gene NANOG hESC enhancer GRCh37_chr15:81841057-81841558 Neighboring gene uncharacterized LOC102723985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:81943819-81944319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:81944380-81944880

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations.
    EBI GWAS Catalog

    HIV-1 interactions

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ16806, FLJ42735, FLJ44234

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables CD4 receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables CD4 receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables cytokine activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Flemming body IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    located_in extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
     
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    pro-interleukin-16
    Names
    lymphocyte chemoattractant factor
    neuronal interleukin 16
    prointerleukin 16

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_029933.2 RefSeqGene

      Range
      19169..136348
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001172128.2NP_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)
      AC036196, AC103858
      Consensus CDS
      CCDS53966.1
      UniProtKB/TrEMBL
      I7GGY3
      Related
      ENSP00000378155.2, ENST00000394660.6
      Conserved Domains (2) summary
      smart00228
      Location:12331319
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:217300
      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) ...
    2. NM_001352684.2NP_001339613.1  pro-interleukin-16 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC036196, AC103858
      UniProtKB/TrEMBL
      Q53HR8
      Conserved Domains (3) summary
      smart00228
      Location:624710
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:501578
      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:250345
      COG1615; Uncharacterized membrane protein, UPF0182 family [Function unknown]
    3. NM_001352685.2NP_001339614.1  pro-interleukin-16 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC036196, AC103858
      UniProtKB/TrEMBL
      I7GGY3
      Conserved Domains (3) summary
      smart00228
      Location:10631149
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:47130
      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:690785
      COG1615; Uncharacterized membrane protein, UPF0182 family [Function unknown]
    4. NM_001352686.2NP_001339615.1  pro-interleukin-16 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC036196, AC103858
      UniProtKB/TrEMBL
      I7GGY3
      Conserved Domains (3) summary
      smart00228
      Location:12841370
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:268351
      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:9111006
      COG1615; Uncharacterized membrane protein, UPF0182 family [Function unknown]
    5. NM_004513.6NP_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
      Consensus CDS
      CCDS10317.1
      UniProtKB/TrEMBL
      Q9UME6
      Related
      ENSP00000378147.2, ENST00000394652.6
      Conserved Domains (3) summary
      smart00228
      Location:533619
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:410487
      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:347432
      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. ...
    6. NM_172217.5NP_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
      Consensus CDS
      CCDS42069.1
      UniProtKB/Swiss-Prot
      A6NM20, A8MU65, B5TY35, B9EGR6, H3BVH5, Q14005, Q16435, Q6VVE6, Q6ZMQ7, Q9UP18
      UniProtKB/TrEMBL
      I7GGY3
      Related
      ENSP00000508085.1, ENST00000683961.1
      Conserved Domains (2) summary
      smart00228
      Location:12341320
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:217300
      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) ...

    RNA

    1. NR_148035.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC036196, AC103858

    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

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      81182712..81314058
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432447.1XP_047288403.1  pro-interleukin-16 isoform X1

    2. XM_047432448.1XP_047288404.1  pro-interleukin-16 isoform X2

    3. XM_047432449.1XP_047288405.1  pro-interleukin-16 isoform X3

    4. XM_047432450.1XP_047288406.1  pro-interleukin-16 isoform X4

      UniProtKB/TrEMBL
      A0A8C8KBU6
      Related
      ENSP00000302935.5, ENST00000302987.10
    5. XM_047432451.1XP_047288407.1  pro-interleukin-16 isoform X5

    6. XM_047432452.1XP_047288408.1  pro-interleukin-16 isoform X6

    7. XM_047432455.1XP_047288411.1  pro-interleukin-16 isoform X9

    8. XM_047432458.1XP_047288414.1  pro-interleukin-16 isoform X12

      Related
      ENSP00000453250.1, ENST00000559383.5
    9. XM_047432453.1XP_047288409.1  pro-interleukin-16 isoform X7

      UniProtKB/Swiss-Prot
      A6NM20, A8MU65, B5TY35, B9EGR6, H3BVH5, Q14005, Q16435, Q6VVE6, Q6ZMQ7, Q9UP18
    10. XM_047432454.1XP_047288410.1  pro-interleukin-16 isoform X8

    11. XM_047432456.1XP_047288412.1  pro-interleukin-16 isoform X10

    12. XM_047432457.1XP_047288413.1  pro-interleukin-16 isoform X11

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      79045899..79178128
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377851.1XP_054233826.1  pro-interleukin-16 isoform X12

    2. XM_054377848.1XP_054233823.1  pro-interleukin-16 isoform X9

    3. XM_054377840.1XP_054233815.1  pro-interleukin-16 isoform X3

    4. XM_054377841.1XP_054233816.1  pro-interleukin-16 isoform X4

      UniProtKB/TrEMBL
      A0A8C8KBU6
    5. XM_054377842.1XP_054233817.1  pro-interleukin-16 isoform X14

    6. XM_054377843.1XP_054233818.1  pro-interleukin-16 isoform X15

    7. XM_054377839.1XP_054233814.1  pro-interleukin-16 isoform X13

    8. XM_054377838.1XP_054233813.1  pro-interleukin-16 isoform X7

      UniProtKB/Swiss-Prot
      A6NM20, A8MU65, B5TY35, B9EGR6, H3BVH5, Q14005, Q16435, Q6VVE6, Q6ZMQ7, Q9UP18
    9. XM_054377844.1XP_054233819.1  pro-interleukin-16 isoform X7

      UniProtKB/Swiss-Prot
      A6NM20, A8MU65, B5TY35, B9EGR6, H3BVH5, Q14005, Q16435, Q6VVE6, Q6ZMQ7, Q9UP18
    10. XM_054377846.1XP_054233821.1  pro-interleukin-16 isoform X17

    11. XM_054377845.1XP_054233820.1  pro-interleukin-16 isoform X16

    12. XM_054377847.1XP_054233822.1  pro-interleukin-16 isoform X8

    13. XM_054377849.1XP_054233824.1  pro-interleukin-16 isoform X10

    14. XM_054377850.1XP_054233825.1  pro-interleukin-16 isoform X11