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    CLCF1 cardiotrophin like cytokine factor 1 [ Homo sapiens (human) ]

    Gene ID: 23529, updated on 11-Apr-2024

    Summary

    Official Symbol
    CLCF1provided by HGNC
    Official Full Name
    cardiotrophin like cytokine factor 1provided by HGNC
    Primary source
    HGNC:HGNC:17412
    See related
    Ensembl:ENSG00000175505 MIM:607672; AllianceGenome:HGNC:17412
    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
    CLC; NR6; BSF3; NNT1; BSF-3; CISS2; NNT-1
    Summary
    This gene is a member of the glycoprotein (gp)130 cytokine family and encodes cardiotrophin-like cytokine factor 1 (CLCF1). CLCF1 forms a heterodimer complex with cytokine receptor-like factor 1 (CRLF1). This dimer competes with ciliary neurotrophic factor (CNTF) for binding to the ciliary neurotrophic factor receptor (CNTFR) complex, and activates the Jak-STAT signaling cascade. CLCF1 can be actively secreted from cells by forming a complex with soluble type I CRLF1 or soluble CNTFR. CLCF1 is a potent neurotrophic factor, B-cell stimulatory agent and neuroendocrine modulator of pituitary corticotroph function. Defects in CLCF1 cause cold-induced sweating syndrome 2 (CISS2). This syndrome is characterized by a profuse sweating after exposure to cold as well as congenital physical abnormalities of the head and spine. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2009]
    Expression
    Broad expression in gall bladder (RPKM 9.3), endometrium (RPKM 7.5) and 21 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CLCF1 in Genome Data Viewer
    Location:
    11q13.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (67364168..67374177, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (67358280..67368294, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67131639..67141648, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100130987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67119697-67120279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67120280-67120861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3625 Neighboring gene DNA polymerase delta 4, accessory subunit Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5089 Neighboring gene RN7SK pseudogene 239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67134979-67135478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67146845-67147566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5090 Neighboring gene hESC enhancers GRCh37_chr11:67158624-67159539 and GRCh37_chr11:67159574-67160078 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67164978-67165559 Neighboring gene RNA, U6 small nuclear 1238, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67165560-67166140 Neighboring gene RAD9 checkpoint clamp component A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3630 Neighboring gene protein phosphatase 1 catalytic subunit alpha

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: POLD4

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to ciliary neurotrophic factor receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ciliary neurotrophic factor receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to cytokine activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cytokine activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables growth factor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in B cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell surface receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell surface receptor signaling pathway via JAK-STAT IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell surface receptor signaling pathway via JAK-STAT ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cytokine-mediated signaling pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of neuron apoptotic process IDA
    Inferred from Direct Assay
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of astrocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of immunoglobulin production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of isotype switching to IgE isotypes ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of CRLF-CLCF1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of CRLF-CLCF1 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in extracellular region IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    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 stimulatory factor 3
    B-cell-stimulating factor 3
    CRLF1 associated cytokine-like factor 1
    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.

    Genomic

    1. NG_013377.1 RefSeqGene

      Range
      5580..15010
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001166212.2NP_001159684.1  cardiotrophin-like cytokine factor 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159684.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus when compared to isoform 1.
      Source sequence(s)
      AK298052, BC012939, DC393345
      Consensus CDS
      CCDS53666.1
      UniProtKB/Swiss-Prot
      Q9UBD9
      Related
      ENSP00000434122.1, ENST00000533438.1
      Conserved Domains (1) summary
      cl21565
      Location:46202
      LIF_OSM; LIF / OSM family
    2. NM_013246.3NP_037378.1  cardiotrophin-like cytokine factor 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_037378.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Though this isoform has a predicted signal peptide at amino acids 1-27, experiments show it is retained within the cell.
      Source sequence(s)
      BC012939, BM846622
      Consensus CDS
      CCDS31617.1
      UniProtKB/Swiss-Prot
      B4DNT4, Q6NZA4, Q9UBD9
      Related
      ENSP00000309338.7, ENST00000312438.8
      Conserved Domains (1) summary
      cl21565
      Location:56212
      LIF_OSM; LIF / OSM family

    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

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      67364168..67374177 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      67358280..67368294 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)