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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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See CKLF-CMTM1 in Genome Data Viewer
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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