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

    Gene ID: 9560, updated on 17-Sep-2024

    Summary

    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
    NEW
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General protein information

    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)

    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_001291468.2NP_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:3184
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
    2. NM_001291469.2NP_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:3164
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
    3. NM_001291470.2NP_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:3164
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
    4. NM_001291471.2NP_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:3164
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
    5. NM_001291472.2NP_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:3181
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
    6. NM_001291473.2NP_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:3165
      SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
    7. NM_001291474.2NP_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_001291475.2NP_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:3172
      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_054328432.1XP_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
      UniProtKB/TrEMBL
      B7ZW36
      Related
      ENSP00000483609.1, ENST00000620250.1
    2. XM_054328433.1XP_054184408.1  C-C motif chemokine 4-like isoform X2

      UniProtKB/TrEMBL
      Q6JSE0

    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_054329390.1XP_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
      UniProtKB/TrEMBL
      B7ZW36
    2. XM_054329391.1XP_054185366.1  C-C motif chemokine 4-like isoform X2

      UniProtKB/TrEMBL
      Q6JSE0

    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_054330085.1XP_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
      UniProtKB/TrEMBL
      B7ZW36
    2. XM_054330086.1XP_054186061.1  C-C motif chemokine 4-like isoform X2

      UniProtKB/TrEMBL
      Q6JSE0

    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_054317888.1XP_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
      UniProtKB/TrEMBL
      B7ZW36
    2. XM_054317889.1XP_054173864.1  C-C motif chemokine 4-like isoform X2

      UniProtKB/TrEMBL
      Q6JSE0

    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.