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

    Gene ID: 56708, updated on 9-Dec-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 cell surface receptor signaling pathway via STAT; positive regulation of B cell activation; and positive regulation of astrocyte differentiation. Acts upstream of or within B cell differentiation and cell surface 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, Dec 2024]
    Expression
    Broad expression in spleen adult (RPKM 32.4), mammary gland adult (RPKM 16.1) and 15 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Clcf1 in Genome Data Viewer
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    contributes_to ciliary neurotrophic factor receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    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
     
    enables signaling receptor binding ISS
    Inferred from Sequence or Structural Similarity
    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 cell surface receptor signaling pathway via 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 ISS
    Inferred from Sequence or Structural Similarity
    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 cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    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 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 IEA
    Inferred from Electronic Annotation
    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 ISS
    Inferred from Sequence or Structural Similarity
    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 region ISS
    Inferred from Sequence or Structural Similarity
    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)

    NEW Try the new Transcript table

    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)