Cklf chemokine-like factor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cklfprovided by MGI
Official Full Name: chemokine-like factorprovided by MGI
Primary source: MGI:MGI:1922708
See related: Ensembl:ENSMUSG00000054400 AllianceGenome:MGI:1922708
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: C32; CKLF1; CKLF3; CKLF4; CKLF5; Cklf2; Cklf6; UCK-1; HSPC224; 1700001C14Rik; 1810018M11Rik; A730028G07Rik
Summary: Predicted to enable chemokine activity. Predicted to be involved in leukocyte chemotaxis and secretion by cell. Predicted to act upstream of or within chemotaxis. Predicted to be located in extracellular region. Predicted to be integral component of membrane. Orthologous to human CKLF (chemokine like factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in testis adult (RPKM 19.7), limb E14.5 (RPKM 4.0) and 15 other tissues See more
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Genomic context

Location:: 8; 8 D3

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (104977493..104992642)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (104250861..104266010)

Chromosome 8 - NC_000074.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CKLF induces microglial activation via triggering defective mitophagy and mitochondrial dysfunction.
Title: CKLF induces microglial activation via triggering defective mitophagy and mitochondrial dysfunction.
NF-kappaB signaling pathway was involved in the asthmatic change induced by CKLF1, among which CCR4 might play a crucial role
Title: The chemokine-like factor 1 induces asthmatic pathological change by activating nuclear factor-κB signaling pathway.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chemokine activity	ISO Inferred from Sequence Orthology more info
enables cytokine activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in leukocyte chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in lymphocyte chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in macrophage chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in neutrophil chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in secretion by cell	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in extracellular region	ISO Inferred from Sequence Orthology more info
located_in extracellular space	IEA Inferred from Electronic Annotation more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: chemokine-like factor

Names: chemokine-like factor 2; chemokine-like factor 4; chemokine-like factor 6

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_001037841.3 → NP_001032930.1 chemokine-like factor isoform 4

See identical proteins and their annotated locations for NP_001032930.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an exon in the 3' coding region and contains an alternate terminal exon, compared to variant 1. This results in a protein (isoform 4) that is shorter and contains a distinct C-terminus.

Source sequence(s)

AC115718, AK032759

Consensus CDS

CCDS40449.1

UniProtKB/TrEMBL

A0A1D5RLG8

Related

ENSMUSP00000096064.5, ENSMUST00000098464.6
NM_001286383.1 → NP_001273312.1 chemokine-like factor isoform 5

See identical proteins and their annotated locations for NP_001273312.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region. This results in a shorter protein (isoform 5).

Source sequence(s)

AC115718, AY046597, BE630757

Consensus CDS

CCDS85592.1

UniProtKB/Swiss-Prot

Q9DAS1

Related

ENSMUSP00000148697.2, ENSMUST00000211809.2
NM_029295.3 → NP_083571.1 chemokine-like factor isoform 1

See identical proteins and their annotated locations for NP_083571.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC115718, AK046397, BE630757

Consensus CDS

CCDS40450.1

UniProtKB/Swiss-Prot

Q3T9V7, Q8BUC3, Q91ZA4, Q923S4, Q923S5, Q9DAS1

Related

ENSMUSP00000034342.6, ENSMUST00000034342.13

Conserved Domains (1) summary

cl04571
Location:13 → 127

MARVEL; Membrane-associating domain

RNA

NR_104433.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (6) contains an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC115718, AC121275, AK046397, BE630757

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000074.7 Reference GRCm39 C57BL/6J

Range

104977493..104992642

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030243826.2 → XP_030099686.1 chemokine-like factor isoform X1
XM_030243827.2 → XP_030099687.1 chemokine-like factor isoform X2

Related

ENSMUSP00000148816.2, ENSMUST00000212410.2

RNA

XR_003947352.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001037840.1: Suppressed sequence

Description

NM_001037840.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
NM_029313.1: Suppressed sequence

Description

NM_029313.1: This RefSeq was permanently suppressed because it is primarily intronic sequence. The 3' end appears to be falsely primed off of an a-rich region of the genome.