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

Gene ID: 23529, updated on 2-Nov-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
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (67364168..67374177, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (67358280..67368294, complement)
RS_2024_09 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 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 cell surface receptor signaling pathway via STAT IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell surface receptor signaling pathway via STAT TAS
Traceable Author Statement
more info
PubMed 
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
 
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)

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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.

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_2024_08

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)