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

Gene ID: 9560, updated on 23-Nov-2021

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
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
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Genomic context

See CCL4L2 in Genome Data Viewer
Location:
17q12
Exon count:
3
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (36211063..36212873)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (34538465..34540275)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene nitric oxide synthase 2, inducible pseudogene Neighboring gene TBC1 domain family member 3B Neighboring gene C-C motif chemokine ligand 3 like 3 Neighboring gene uncharacterized LOC105371747 Neighboring gene TBC1 domain family member 3I

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

Associated conditions

Description Tests
A genome-wide association study identifies protein quantitative trait loci (pQTLs).
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC104419

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)

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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)

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

    See identical proteins and their annotated locations for NP_001278397.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (CCL4L2) encodes isoform 1.
    Source sequence(s)
    AY766450
    Consensus CDS
    CCDS32627.2
    UniProtKB/Swiss-Prot
    Q8NHW4
    Related
    ENSP00000479354.1, ENST00000620576.4
    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

    See identical proteins and their annotated locations for NP_001278398.1

    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

    See identical proteins and their annotated locations for NP_001278399.1

    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

    See identical proteins and their annotated locations for NP_001278400.1

    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/Swiss-Prot
    Q8NHW4
    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

    See identical proteins and their annotated locations for NP_001278401.1

    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/Swiss-Prot
    Q8NHW4
    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

    See identical proteins and their annotated locations for NP_001278402.1

    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/Swiss-Prot
    Q8NHW4
    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

    See identical proteins and their annotated locations for NP_001278403.1

    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
    UniProtKB/Swiss-Prot
    Q8NHW4
    Related
    ENSP00000484455.1, ENST00000613173.4
  8. NM_001291475.2NP_001278404.1  C-C motif chemokine 4-like isoform 7 precursor

    See identical proteins and their annotated locations for NP_001278404.1

    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
    UniProtKB/Swiss-Prot
    Q8NHW4
    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: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

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

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_187614.1 Reference GRCh38.p13 ALT_REF_LOCI_1

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

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_187661.1 Reference GRCh38.p13 ALT_REF_LOCI_2

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

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.
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