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Clcf1 cardiotrophin-like cytokine factor 1 [ Mus musculus (house mouse) ]

Gene ID: 56708, updated on 12-May-2024

Summary

Official Symbol
Clcf1provided by MGI
Official Full Name
cardiotrophin-like cytokine factor 1provided by MGI
Primary source
MGI:MGI:1930088
See related
Ensembl:ENSMUSG00000040663 AllianceGenome:MGI:1930088
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
CLC; Bsf3; BSF-3; NNT-1
Summary
Enables cytokine activity. Involved in positive regulation of B cell activation; positive regulation of astrocyte differentiation; and positive regulation of tyrosine phosphorylation of STAT protein. Acts upstream of or within B cell differentiation and receptor signaling pathway via JAK-STAT. Predicted to be located in extracellular space. Predicted to be part of CNTFR-CLCF1 complex and CRLF-CLCF1 complex. Predicted to be active in extracellular region. Is expressed in several structures, including alimentary system; central nervous system; lung; metanephros; and skeletal musculature. Human ortholog(s) of this gene implicated in cold-induced sweating syndrome 2. Orthologous to human CLCF1 (cardiotrophin like cytokine factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in spleen adult (RPKM 32.4), mammary gland adult (RPKM 16.1) and 15 other tissues See more
Orthologs
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Genomic context

Location:
19 A; 19 3.91 cM
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (4264479..4273548)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (4214238..4223505)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E11010 Neighboring gene protein phosphatase 1 catalytic subunit alpha Neighboring gene STARR-positive B cell enhancer ABC_E4257 Neighboring gene RAD9 checkpoint clamp component A Neighboring gene RIKEN cDNA 1500032F14 gene Neighboring gene predicted gene, 30082 Neighboring gene STARR-positive B cell enhancer ABC_E11667 Neighboring gene predicted gene, 45928 Neighboring gene STARR-positive B cell enhancer ABC_E969 Neighboring gene polymerase (DNA-directed), delta 4 Neighboring gene STARR-positive B cell enhancer ABC_E5676 Neighboring gene microRNA 6985 Neighboring gene slingshot protein phosphatase 3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 
  • Targeted (3)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough Gm45928

Readthrough gene: Gm45928, Included gene: Pold4

Clone Names

  • MGC129162, MGC129163

Gene Ontology Provided by MGI

Function Evidence Code Pubs
contributes_to ciliary neurotrophic factor receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables ciliary neurotrophic factor receptor binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to ciliary neurotrophic factor receptor binding TAS
Traceable Author Statement
more info
PubMed 
enables cytokine activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables cytokine activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to cytokine activity ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables signaling receptor binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within B cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within cell surface receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell surface receptor signaling pathway via JAK-STAT IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within cell surface receptor signaling pathway via JAK-STAT IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of motor neuron apoptotic process NAS
Non-traceable Author Statement
more info
PubMed 
involved_in negative regulation of neuron apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of neuron apoptotic process NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of B cell proliferation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of B cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of astrocyte differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of corticotropin-releasing hormone secretion TAS
Traceable Author Statement
more info
PubMed 
involved_in positive regulation of immunoglobulin production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of isotype switching to IgE isotypes IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of type 2 immune response NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of tyrosine phosphorylation of STAT protein IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of tyrosine phosphorylation of STAT protein IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of tyrosine phosphorylation of STAT protein ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of ERK1 and ERK2 cascade TAS
Traceable Author Statement
more info
PubMed 
involved_in regulation of inflammatory response NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
part_of CNTFR-CLCF1 complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of CNTFR-CLCF1 complex ISO
Inferred from Sequence Orthology
more info
 
part_of CRLF-CLCF1 complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of CRLF-CLCF1 complex ISO
Inferred from Sequence Orthology
more info
 
part_of CRLF-CLCF1 complex TAS
Traceable Author Statement
more info
PubMed 
is_active_in extracellular region IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular region ISO
Inferred from Sequence Orthology
more info
 
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
cardiotrophin-like cytokine factor 1
Names
B-cell stimulating factor 3
neurotrophin-1/B-cell stimulating factor-3
novel neurotrophin-1

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_001310038.3NP_001296967.1  cardiotrophin-like cytokine factor 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001296967.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' region resulting in differences in the 5' UTR and translation initiation from a downstream start codon, compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1. Both variants 2 and 3 encode the same protein (isoform 2).
    Source sequence(s)
    AC140073
    UniProtKB/TrEMBL
    Q3TC09, Q3TM06
    Conserved Domains (1) summary
    cl21565
    Location:46202
    LIF_OSM; LIF / OSM family
  2. NM_001310039.2NP_001296968.1  cardiotrophin-like cytokine factor 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001296968.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon resulting in differences in the 5' UTR and translation initiation from a downstream start codon, compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1. Both variants 2 and 3 encode the same protein (isoform 2).
    Source sequence(s)
    AC140073
    UniProtKB/TrEMBL
    Q3TC09, Q3TM06
    Conserved Domains (1) summary
    cl21565
    Location:46202
    LIF_OSM; LIF / OSM family
  3. NM_019952.6NP_064336.1  cardiotrophin-like cytokine factor 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_064336.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC140073
    Consensus CDS
    CCDS29423.1
    UniProtKB/Swiss-Prot
    Q3SXK2, Q9QZM3
    UniProtKB/TrEMBL
    Q3TC09
    Related
    ENSMUSP00000045562.7, ENSMUST00000046506.7
    Conserved Domains (1) summary
    cl21565
    Location:56212
    LIF_OSM; LIF / OSM family

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

  1. NC_000085.7 Reference GRCm39 C57BL/6J

    Range
    4264479..4273548
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)