CCL4L1 C-C motif chemokine ligand 4 like 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCL4L1provided by HGNC
Official Full Name: C-C motif chemokine ligand 4 like 1provided by HGNC
Primary source: HGNC:HGNC:10631
See related: MIM:603782; AllianceGenome:HGNC:10631
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: LAG1; CCL4L; LAG-1; SCYA4L; AT744.2; SCYA4L1; SCYA4L2; MIP-1-beta
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. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2014]
Annotation information: Annotation category: only annotated on alternate loci in reference assembly; 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]
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Genomic context

Location:: 17q12

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17 (ALT_REF_LOCI_2)	NT_187661.1 (266611..268581)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (37384271..37386241)

NT_187661.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
PCR results show that lower copy numbers of CCL4L1 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.
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.
multiple copies of CCL3L1 and CCL4L1 present in a single diploid genome are the result of segmental duplication at chromosome 17q12
Title: CCL3L1 and CCL4L1 chemokine genes are located in a segmental duplication at chromosome 17q12.

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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 upregulates the expression of chemokine (C-C motif) ligand 4-like 1 (CCL4L1) in human B cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH17517 (e-PCR)
- UniSTS:45079

STS-M69203 (e-PCR)
- UniSTS:25645

ovineDNA_CCL4 (e-PCR)
- UniSTS:514616

PMC152049P1 (e-PCR)
- UniSTS:271198

Clone Names

MGC163328, MGC163330, MGC177931, MGC180204, MGC182047, MGC182061, MGC183187, MGC198579

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables CCR chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables chemokine activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemokine-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in eosinophil chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: C-C motif chemokine 4-like

Names: CC chemokine ligand 4L1; Lymphocyte activation gene 1 protein; Macrophage inflammatory protein 1-beta; Monocyte adherence-induced protein 5-alpha; Small-inducible cytokine A4-like; chemokine (C-C motif) ligand 4-like 1, telomeric; macrophage inflammatory protein-1b2; small inducible cytokine A4-like

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)

NM_207007.4 → NP_996890.1 C-C motif chemokine 4-like precursor

See identical proteins and their annotated locations for NP_996890.1

Status: REVIEWED

Description

Transcript Variant: This variant (CCL4L) represents the longer transcript and encodes the supported protein.

Source sequence(s)

AC131056

UniProtKB/Swiss-Prot

B2RUZ3, B7ZMA8, Q50EM1, Q50EM2, Q50EM3, Q50EM4, Q50EM5, Q50EM6, Q50EM7, Q50EM8, Q569J2, Q6NSB0, Q8NHW4

UniProtKB/TrEMBL

B7ZW36

Conserved Domains (1) summary

pfam00048
Location:32 → 86

IL8; Small cytokines (intecrine/chemokine), interleukin-8 like

RNA

NR_111969.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (CCL4Ldelta2, also known as 4L1d2) lacks an alternate internal exon, compared to variant CCL4L. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AY766449, BC171857, BU626856