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    CHLSN cholesin [ Homo sapiens (human) ]

    Gene ID: 84310, updated on 21-Nov-2024

    Summary

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    Official Symbol
    CHLSNprovided by HGNC
    Official Full Name
    cholesinprovided by HGNC
    Primary source
    HGNC:HGNC:22421
    See related
    Ensembl:ENSG00000146540 AllianceGenome:HGNC:22421
    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
    Also known as
    C7orf50; YCR016W
    Summary
    Enables hormone activity. Involved in negative regulation of cholesterol biosynthetic process. Is active in extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 5.2), brain (RPKM 3.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CHLSN in Genome Data Viewer
    Location:
    7p22.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (977964..1138257, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (1082961..1240814, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (1017600..1177893, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ArfGAP with dual PH domains 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17830 Neighboring gene uncharacterized LOC124901569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:994600-995209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1002516-1003103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1006706-1007206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1007207-1007707 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1014408-1015290 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1015291-1016171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1028403-1029003 Neighboring gene cytochrome c oxidase assembly factor COX19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1036874-1037414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1038871-1039460 Neighboring gene uncharacterized LOC124901570 Neighboring gene cytochrome P450 family 2 subfamily W member 1 Neighboring gene nonconserved acetylation island sequence 100 enhancer Neighboring gene hESC enhancers GRCh37_chr7:1067181-1067915 and GRCh37_chr7:1067916-1068649 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1075522-1076044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1076045-1076566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1080290-1080797 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1081305-1081812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1083301-1083856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17842 Neighboring gene microRNA 339 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1091635-1092615 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr7:1095105-1095810 and GRCh37_chr7:1095811-1096516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25486 Neighboring gene Sharpr-MPRA regulatory region 11358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25487 Neighboring gene G protein-coupled receptor 146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1109435-1110218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1110219-1111001 Neighboring gene CHLSN antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1135129-1135838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:1140145-1140645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1147881-1148424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1149827-1150667 Neighboring gene G protein-coupled estrogen receptor 1 Neighboring gene uncharacterized LOC102723758 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:1156037-1157236 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_97501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17845 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1185078-1185771 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:1198934-1199448 Neighboring gene hESC enhancers GRCh37_chr7:1199449-1199961 and GRCh37_chr7:1199962-1200475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:1200476-1200988 Neighboring gene zinc finger AN1-type containing 2A Neighboring gene ZFAND2A divergent transcript

    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. Cholesin receptor signalling is active in cardiovascular system-associated adipose tissue and correlates with SGLT2i treatment in patients with diabetes. Ryk A, et al. Cardiovasc Diabetol, 2024 Jun 20. PMID 38902687, Free PMC Article
    2. Epigenome-wide association study in whole blood on type 2 diabetes among sub-Saharan African individuals: findings from the RODAM study. Meeks KAC, et al. Int J Epidemiol, 2019 Feb 1. PMID 30107520, Free PMC Article
    3. A gut-derived hormone regulates cholesterol metabolism. Hu X, et al. Cell, 2024 Mar 28. PMID 38503280
    4. Joint influence of small-effect genetic variants on human longevity. Yashin AI, et al. Aging (Albany NY), 2010 Sep. PMID 20834067, Free PMC Article
    5. Protein microarray analysis identifies human cellular prion protein interactors. Satoh J, et al. Neuropathol Appl Neurobiol, 2009 Feb. PMID 18482256

    See all (95) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A gut-derived hormone regulates cholesterol metabolism.
      Title: A gut-derived hormone regulates cholesterol metabolism.
    2. Three ubiquitous methylation loci were consistently and strongly associated with type 2 diabetes in Ghanaians: TXNIP, C7orf50 and CPT1A
      Title: Epigenome-wide association study in whole blood on type 2 diabetes among sub-Saharan African individuals: findings from the RODAM study.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Joint influence of small-effect genetic variants on human longevity.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC11257

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables hormone activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of cholesterol biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein cholesin
    Names
    uncharacterized protein C7orf50

    NCBI Reference Sequences (RefSeq)

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    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_001134395.1 → NP_001127867.1  protein cholesin isoform a

      See identical proteins and their annotated locations for NP_001127867.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-4 all encode the same isoform (a).
      Source sequence(s)
      BC006224, BM676072, CN261680
      Consensus CDS
      CCDS5320.1
      UniProtKB/Swiss-Prot
      Q9BRJ6
      UniProtKB/TrEMBL
      C9JQV0
      Conserved Domains (1) summary
      pfam10180
      Location:104 → 165
      DUF2373; uncharacterized conserved protein (DUF2373)

    2. NM_001134396.1 → NP_001127868.1  protein cholesin isoform a

      See identical proteins and their annotated locations for NP_001127868.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-4 all encode the same isoform (a).
      Source sequence(s)
      BC006224, BM676072, BM763235
      Consensus CDS
      CCDS5320.1
      UniProtKB/Swiss-Prot
      Q9BRJ6
      UniProtKB/TrEMBL
      C9JQV0
      Related
      ENSP00000380288.2, ENST00000397100.6
      Conserved Domains (1) summary
      pfam10180
      Location:104 → 165
      DUF2373; uncharacterized conserved protein (DUF2373)

    3. NM_001318252.2 → NP_001305181.1  protein cholesin isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1-4 all encode the same isoform (a).
      Source sequence(s)
      AC091729, AF495721, BC006224
      Consensus CDS
      CCDS5320.1
      UniProtKB/Swiss-Prot
      Q9BRJ6
      UniProtKB/TrEMBL
      C9JQV0
      Related
      ENSP00000380286.3, ENST00000397098.8
      Conserved Domains (1) summary
      pfam10180
      Location:104 → 165
      DUF2373; uncharacterized conserved protein (DUF2373)

    4. NM_001350968.1 → NP_001337897.1  protein cholesin isoform b

      Status: VALIDATED

      Source sequence(s)
      AC073957, AC091729
      UniProtKB/TrEMBL
      C9JQV0
      Conserved Domains (1) summary
      pfam10180
      Location:104 → 165
      DUF2373; Uncharacterized conserved protein (DUF2373)

    5. NM_001350969.2 → NP_001337898.1  protein cholesin isoform c

      Status: VALIDATED

      Source sequence(s)
      AC073957
      UniProtKB/TrEMBL
      H7C0T1
      Conserved Domains (1) summary
      pfam10180
      Location:90 → 151
      DUF2373; Uncharacterized conserved protein (DUF2373)

    6. NM_001350970.1 → NP_001337899.1  protein cholesin isoform d

      Status: VALIDATED

      Source sequence(s)
      AC091729

    7. NM_001424325.1 → NP_001411254.1  protein cholesin isoform d

      Status: VALIDATED

      Source sequence(s)
      AC073957, AC091729

    8. NM_001424326.1 → NP_001411255.1  protein cholesin isoform e

      Status: VALIDATED

      Source sequence(s)
      AC073957, AC091729

    9. NM_001424327.1 → NP_001411256.1  protein cholesin isoform f

      Status: VALIDATED

      Source sequence(s)
      AC073957

    10. NM_001424329.1 → NP_001411258.1  protein cholesin isoform g

      Status: VALIDATED

      Source sequence(s)
      AC073957

    11. NM_001424333.1 → NP_001411262.1  protein cholesin isoform a

      Status: VALIDATED

      Source sequence(s)
      CP068271
      UniProtKB/Swiss-Prot
      Q9BRJ6

    12. NM_001424334.1 → NP_001411263.1  protein cholesin isoform a

      Status: VALIDATED

      Source sequence(s)
      CP068271
      UniProtKB/Swiss-Prot
      Q9BRJ6

    13. NM_001424335.1 → NP_001411264.1  protein cholesin isoform b

      Status: VALIDATED

      Source sequence(s)
      CP068271

    14. NM_001424336.1 → NP_001411265.1  protein cholesin isoform e

      Status: VALIDATED

      Source sequence(s)
      CP068271

    15. NM_001424337.1 → NP_001411266.1  protein cholesin isoform d

      Status: VALIDATED

      Source sequence(s)
      CP068271

    16. NM_032350.5 → NP_115726.1  protein cholesin isoform a

      See identical proteins and their annotated locations for NP_115726.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1-4 all encode the same isoform (a).
      Source sequence(s)
      BC006224, BM676072
      Consensus CDS
      CCDS5320.1
      UniProtKB/Swiss-Prot
      Q9BRJ6
      UniProtKB/TrEMBL
      C9JQV0
      Related
      ENSP00000350011.5, ENST00000357429.10
      Conserved Domains (1) summary
      pfam10180
      Location:104 → 165
      DUF2373; uncharacterized conserved protein (DUF2373)

    RNA

    1. NR_134537.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks two 5' exons and uses an alternate 5'-terminal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      BC006224, BM762287
      Related
      ENST00000412051.5

    2. NR_134538.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks several exons and contains two alternate exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC073957, BC025971, BF129057, BQ006497
      Related
      ENST00000465681.1

    3. NR_146964.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    4. NR_146965.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    5. NR_146966.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    6. NR_146967.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    7. NR_156697.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    8. NR_188522.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    9. NR_188523.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    10. NR_188524.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    11. NR_188525.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    12. NR_188526.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    13. NR_188533.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC073957

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      977964..1138257 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      1082961..1240814 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRJ6.1 GenPept UniProtKB/Swiss-Prot:Q9BRJ6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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