U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    CCL4L2 C-C motif chemokine ligand 4 like 2 [ Homo sapiens (human) ]

    Gene ID: 9560, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    CCL4L2provided by HGNC
    Official Full Name
    C-C motif chemokine ligand 4 like 2provided by HGNC
    Primary source
    HGNC:HGNC:24066
    See related
    Ensembl:ENSG00000276070 MIM:610757; AllianceGenome:HGNC:24066
    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
    CCL4L; SCYA4L; AT744.2; SCYQ4L2
    Summary
    This gene is one of several cytokine genes that are clustered on the q-arm of chromosome 17. Cytokines are a family of secreted proteins that function in inflammatory and immunoregulatory processes. The protein encoded by this family member is similar to the chemokine (C-C motif) ligand 4 product, which inhibits HIV entry by binding to the cellular receptor CCR5. The copy number of this gene varies among individuals, where most individuals have one to five copies. This gene copy contains a non-consensus splice acceptor site at the 3' terminal exon found in other highly similar gene copies, and it thus uses other alternative splice sites for the 3' terminal exon, resulting in multiple transcript variants. [provided by RefSeq, Apr 2014]
    Annotation information
    Note: In NCBI's Homo sapiens Annotation Release 106, this GeneID (GeneID:388372) was annotated as the CCL4L2 gene copy of this chemokine (C-C motif) ligand 4-like family member, while highly similar GeneID:9560 was annotated as the CCL4L1 gene copy. However, it has now been determined that these gene copies can be distinguished based on 3' terminal exon splice site usage, as described in PubMedID:15843566. Genomic sequence analysis at the annotated locations indicates that GeneID:388372 actually represents the CCL4L1 gene copy, while GeneID:9560 represents the CCL4L2 gene copy. The gene symbols have therefore been switched accordingly. The CCL4L1 gene copy is present only on the ALT_REF_LOCI_2 alternate haplotype of the GRCh38 human reference genome assembly, while the CCL4L2 gene copy is present on the primary chromosome 17 assembly (NC_000017.11) and on both the ALT_REF_LOCI_1 and ALT_REF_LOCI_2 alternate haplotypes. [17 Jun 2014]
    Expression
    Broad expression in bone marrow (RPKM 21.9), gall bladder (RPKM 7.0) and 15 other tissues See more
    Orthologs
    all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See CCL4L2 in Genome Data Viewer
    Location:
    17q12
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (36211063..36212873)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (37158945..37160755)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (34538465..34540275)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC128966684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:34598171-34598682 Neighboring gene uncharacterized LOC128966706 Neighboring gene C-C motif chemokine ligand 3 like 3 Neighboring gene uncharacterized LOC105371747 Neighboring gene TBC1 domain family member 3I Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:34591003-34591504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:34591505-34592004 Neighboring gene uncharacterized LOC102724956

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Copy number variation in the CCL4L gene is associated with susceptibility to acute rejection in lung transplantation. Colobran R, et al. Genes Immun, 2009 Apr. PMID 19148142
    2. Neutrophil extracellular trap production and CCL4L2 expression influence corticosteroid response in asthma. Tsai CH, et al. Sci Transl Med, 2023 Jun 7. PMID 37285400
    3. Association of VEGFA and CCL4L2 polymorphisms with hand-foot skin reaction and survival of regorafenib in Japanese patients with colorectal cancer. Ono K, et al. Cancer Chemother Pharmacol, 2024 Jul. PMID 38459188
    4. Comparison of a quantitative Real-Time PCR assay and droplet digital PCR for copy number analysis of the CCL4L genes. Bharuthram A, et al. Infect Genet Evol, 2014 Jul. PMID 24727646
    5. CCL4L polymorphisms and CCL4/CCL4L serum levels are associated with psoriasis severity. Pedrosa E, et al. J Invest Dermatol, 2011 Sep. PMID 21614014

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association of VEGFA and CCL4L2 polymorphisms with hand-foot skin reaction and survival of regorafenib in Japanese patients with colorectal cancer.
      Title: Association of VEGFA and CCL4L2 polymorphisms with hand-foot skin reaction and survival of regorafenib in Japanese patients with colorectal cancer.
    2. Neutrophil extracellular trap production and CCL4L2 expression influence corticosteroid response in asthma.
      Title: Neutrophil extracellular trap production and CCL4L2 expression influence corticosteroid response in asthma.
    3. identified 13 ADCC-activated genes. Six gene expression assays including 8 of the 13 genes (CCL3, CCL4/CCL4L1/CCL4L2, CD160, IFNG, NR4A3 and XCL1/XCL2) were analyzed in 127 kidney biopsies
      Title: Genes associated with antibody-dependent cell activation are overexpressed in renal biopsies from patients with antibody-mediated rejection.
    4. PCR results show that lower copy numbers of CCL4L2 are observed in the Caucasian population nd higher copy numbers are observed in the Black population of South Africa.
      Title: Comparison of a quantitative Real-Time PCR assay and droplet digital PCR for copy number analysis of the CCL4L genes.
    5. CCL4L1 allele frequency is higher in severe psoriasis, whereas CCL4L2 is more frequent in patients with a milder disease.
      Title: CCL4L polymorphisms and CCL4/CCL4L serum levels are associated with psoriasis severity.
    6. Studies indicate that complete phenotypic impact requires dissecting the combinatorial genomic complexity posed by various proportions of distinct CCL3L and CCL4L genes among individuals.
      Title: Copy number variation in chemokine superfamily: the complex scene of CCL3L-CCL4L genes in health and disease.
    7. higher level of expression at systemic level is associated with protection from HIV-1 infection in women from Benin
      Title: Chemokine expression patterns in the systemic and genital tract compartments are associated with HIV-1 infection in women from Benin.
    8. A combined analysis of CCL4L copy number variation and the rs4796195 CCL4L single nucleotide polymorphism demonstrated that the effect of CCL4L copy number in acute rejection is mainly because of the number of copies of the CCL4L1 allelic variant.
      Title: Copy number variation in the CCL4L gene is associated with susceptibility to acute rejection in lung transplantation.
    9. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Combinatorial content of CCL3L and CCL4L gene copy numbers influence HIV-AIDS susceptibility in Ukrainian children.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Copy number variation in the CCL4L gene is associated with susceptibility to acute rejection in lung transplantation.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

    Go to the top of the page Help

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    EBI GWAS Catalog

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC104419

    General protein information

    Go to the top of the page Help
    Preferred Names
    C-C motif chemokine 4-like
    Names
    MIP-1-beta
    chemokine (C-C motif) ligand 4-like 2
    macrophage inflammatory protein 1-beta
    macrophage inflammatory protein-1b2
    monocyte adherence-induced protein 5-alpha

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    mRNA and Protein(s)

    1. NM_001291468.2 → NP_001278397.1  C-C motif chemokine 4-like isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2) encodes isoform 1.
      Source sequence(s)
      AY766450
      Consensus CDS
      CCDS32627.2
      UniProtKB/TrEMBL
      B7ZW36
      Related
      ENSP00000479354.1, ENST00000620576.5
      Conserved Domains (1) summary
      smart00199
      Location:31 → 84
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)

    2. NM_001291469.2 → NP_001278398.1  C-C motif chemokine 4-like isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2b1) uses an alternate splice site in the 3' terminal exon, and it thus contains an early termination codon and differs in its 3' UTR, compared to variant CCL4L2. The encoded isoform (2) is shorter at the C-terminus, compared to isoform 1. Both variants CCL4L2b1 and CCL4L2b2 encode isoform 2.
      Source sequence(s)
      AY766451
      Consensus CDS
      CCDS76999.1
      UniProtKB/Swiss-Prot
      Q8NHW4
      Related
      ENSP00000481969.1, ENST00000620732.4
      Conserved Domains (1) summary
      smart00199
      Location:31 → 64
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)

    3. NM_001291470.2 → NP_001278399.1  C-C motif chemokine 4-like isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2b2) fails to splice out the 3'-most intron, and it thus contains an early termination codon and differs in its 3' UTR, compared to variant CCL4L2. The encoded isoform (2) is shorter at the C-terminus, compared to isoform 1. Both variants CCL4L2b1 and CCL4L2b2 encode isoform 2.
      Source sequence(s)
      AY766452
      Consensus CDS
      CCDS77004.1
      UniProtKB/Swiss-Prot
      Q8NHW4
      Related
      ENSP00000480089.1, ENST00000617416.4
      Conserved Domains (1) summary
      smart00199
      Location:31 → 64
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)

    4. NM_001291471.2 → NP_001278400.1  C-C motif chemokine 4-like isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2c) uses an alternate splice site in the 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant CCL4L2. The encoded isoform (3) has a distinct C-terminus and is longer than isoform 1.
      Source sequence(s)
      AY766453
      Consensus CDS
      CCDS77001.1
      UniProtKB/TrEMBL
      A0A0J9YWH4
      Related
      ENSP00000479774.1, ENST00000620098.4
      Conserved Domains (1) summary
      smart00199
      Location:31 → 64
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)

    5. NM_001291472.2 → NP_001278401.1  C-C motif chemokine 4-like isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2d) uses an alternate splice site in the 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant CCL4L2. The encoded isoform (4) has a distinct C-terminus and is longer than isoform 1.
      Source sequence(s)
      AY766454
      Consensus CDS
      CCDS77002.1
      UniProtKB/TrEMBL
      A0A0J9YWH4
      Related
      ENSP00000483206.1, ENST00000615418.4
      Conserved Domains (1) summary
      smart00199
      Location:31 → 81
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)

    6. NM_001291473.2 → NP_001278402.1  C-C motif chemokine 4-like isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2e) uses an alternate splice site in the 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant CCL4L2. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AY766455
      Consensus CDS
      CCDS77003.1
      UniProtKB/TrEMBL
      A0A0J9YWH4
      Related
      ENSP00000484498.1, ENST00000610565.4
      Conserved Domains (1) summary
      smart00199
      Location:31 → 65
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)

    7. NM_001291474.2 → NP_001278403.1  C-C motif chemokine 4-like isoform 6 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2bdelta2) lacks an alternate internal exon and uses an alternate splice site in the 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant CCL4L2. The encoded isoform (6) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AY766457
      Consensus CDS
      CCDS77005.1
      Related
      ENSP00000484455.1, ENST00000613173.4

    8. NM_001291475.2 → NP_001278404.1  C-C motif chemokine 4-like isoform 7 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2f) uses an alternate splice site in the 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant CCL4L2. The encoded isoform (7) has a distinct C-terminus and is longer than isoform 1.
      Source sequence(s)
      AY766458
      Consensus CDS
      CCDS77000.1
      Related
      ENSP00000483330.1, ENST00000617405.5
      Conserved Domains (1) summary
      smart00199
      Location:31 → 72
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)

    RNA

    1. NR_111970.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (CCL4L2delta2) lacks an alternate internal exon, compared to variant CCL4L2. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AY766456
      Related
      ENST00000620055.4

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      36211063..36212873
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328432.1 → XP_054184407.1  C-C motif chemokine 4-like isoform X1

      UniProtKB/Swiss-Prot
      B2RUZ3, B7ZMA8, Q50EM1, Q50EM2, Q50EM3, Q50EM4, Q50EM5, Q50EM6, Q50EM7, Q50EM8, Q569J2, Q6NSB0, Q8NHW4
      Related
      ENSP00000483609.1, ENST00000620250.1

    2. XM_054328433.1 → XP_054184408.1  C-C motif chemokine 4-like isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      445967..447777
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329390.1 → XP_054185365.1  C-C motif chemokine 4-like isoform X1

      UniProtKB/Swiss-Prot
      B2RUZ3, B7ZMA8, Q50EM1, Q50EM2, Q50EM3, Q50EM4, Q50EM5, Q50EM6, Q50EM7, Q50EM8, Q569J2, Q6NSB0, Q8NHW4

    2. XM_054329391.1 → XP_054185366.1  C-C motif chemokine 4-like isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_187661.1 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      165200..167010
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330085.1 → XP_054186060.1  C-C motif chemokine 4-like isoform X1

      UniProtKB/Swiss-Prot
      B2RUZ3, B7ZMA8, Q50EM1, Q50EM2, Q50EM3, Q50EM4, Q50EM5, Q50EM6, Q50EM7, Q50EM8, Q569J2, Q6NSB0, Q8NHW4

    2. XM_054330086.1 → XP_054186061.1  C-C motif chemokine 4-like isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      37158945..37160755
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317888.1 → XP_054173863.1  C-C motif chemokine 4-like isoform X1

      UniProtKB/Swiss-Prot
      B2RUZ3, B7ZMA8, Q50EM1, Q50EM2, Q50EM3, Q50EM4, Q50EM5, Q50EM6, Q50EM7, Q50EM8, Q569J2, Q6NSB0, Q8NHW4

    2. XM_054317889.1 → XP_054173864.1  C-C motif chemokine 4-like isoform X2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001001435.2: Suppressed sequence

      Description
      NM_001001435.2: This RefSeq was permanently suppressed because this gene's genomic location lacks the 3' terminal exon splice site, and it cannot produce this transcript variant.
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous