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

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: all
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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	NC_000017.11 (36211063..36212873)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (37158945..37160755)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (34538465..34540275)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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 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.
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.
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.
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.
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.
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.
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.
Neither CCL3L1 nor CCL4L1 gene copy number variation showed appreciable impact on susceptibility to or control of HIV-1 infection.
Title: CCL3L1 and CCL4L1: variable gene copy number in adolescents with and without human immunodeficiency virus type 1 (HIV-1) infection.

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Phenotypes

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

General protein information

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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)

NM_001291468.2 → NP_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/TrEMBL

A0A0G2JLY3, B7ZW36

Related

ENSP00000479354.1, ENST00000620576.4

Conserved Domains (1) summary

smart00199
Location:31 → 84

SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
NM_001291469.2 → NP_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:31 → 64

SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
NM_001291470.2 → NP_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:31 → 64

SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
NM_001291471.2 → NP_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/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)
NM_001291472.2 → NP_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/TrEMBL

A0A0J9YY69

Related

ENSP00000483206.1, ENST00000615418.4

Conserved Domains (1) summary

smart00199
Location:31 → 81

SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
NM_001291473.2 → NP_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/TrEMBL

A0A0J9YY69

Related

ENSP00000484498.1, ENST00000610565.4

Conserved Domains (1) summary

smart00199
Location:31 → 65

SCY; Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)
NM_001291474.2 → NP_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/TrEMBL

A0A0J9YWD1

Related

ENSP00000484455.1, ENST00000613173.4
NM_001291475.2 → NP_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/TrEMBL

A0A0J9YW77

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

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

36211063..36212873

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

445967..447777

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_187661.1 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

165200..167010

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

37158945..37160755

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

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.