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    CKLF-CMTM1 CKLF-CMTM1 readthrough [ Homo sapiens (human) ]

    Gene ID: 100529251, updated on 8-Mar-2024

    Summary

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    Official Symbol
    CKLF-CMTM1provided by HGNC
    Official Full Name
    CKLF-CMTM1 readthroughprovided by HGNC
    Primary source
    HGNC:HGNC:39977
    See related
    Ensembl:ENSG00000254788 AllianceGenome:HGNC:39977
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This locus represents naturally occurring read-through transcription between the neighboring CKLF (chemokine-like factor) and CMTM1 (CKLF-like MARVEL transmembrane domain containing 1) genes on chromosome 16. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Feb 2011]
    Expression
    Broad expression in testis (RPKM 21.3), appendix (RPKM 15.2) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    16q21
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (66552576..66579135)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72346871..72373430)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66586479..66613038)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene brain expressed associated with NEDD4 1 Neighboring gene uncharacterized LOC124903698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7558 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66510981-66511522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66512063-66512603 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66513685-66514224 Neighboring gene BEAN1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66518060-66519040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66521703-66522203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66543229-66544204 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66545181-66546156 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66546157-66547132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66553931-66554431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10940 Neighboring gene thymidine kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10941 Neighboring gene chemokine like factor Neighboring gene CKLF like MARVEL transmembrane domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7562 Neighboring gene CKLF like MARVEL transmembrane domain containing 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66642903-66643714 Neighboring gene CKLF like MARVEL transmembrane domain containing 4 Neighboring gene CKLF like MARVEL transmembrane domain containing 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. Prakash T, et al. PLoS One, 2010 Oct 12. PMID 20967262, Free PMC Article
    2. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    General gene information

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    Readthrough CKLF-CMTM1

    Included genes: CKLF, CMTM1

    Homology

    General protein information

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    Preferred Names
    CKLF-CMTM1 protein

    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_001202509.2 → NP_001189438.1  CKLF-CMTM1 protein isoform 3

      See identical proteins and their annotated locations for NP_001189438.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
      Source sequence(s)
      AC010542, BM929895
      UniProtKB/TrEMBL
      E9PSG2
      Related
      ENSP00000433998.1, ENST00000527729.5

    2. NM_001204098.2 → NP_001191027.1  CKLF-CMTM1 protein isoform 2

      See identical proteins and their annotated locations for NP_001191027.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC010542, FY211334
      UniProtKB/TrEMBL
      A0A087X286
      Related
      ENSP00000484781.1, ENST00000615332.5

    3. NM_001204099.2 → NP_001191028.1  CKLF-CMTM1 protein isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC010542, FY212695
      UniProtKB/TrEMBL
      A0A087WVB3
      Related
      ENSP00000479319.1, ENST00000616804.5

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      66552576..66579135
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      72346871..72373430
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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