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    PSORS1C3 psoriasis susceptibility 1 candidate 3 [ Homo sapiens (human) ]

    Gene ID: 100130889, updated on 17-Sep-2024

    Summary

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    Official Symbol
    PSORS1C3provided by HGNC
    Official Full Name
    psoriasis susceptibility 1 candidate 3provided by HGNC
    Primary source
    HGNC:HGNC:17203
    See related
    MIM:618690; AllianceGenome:HGNC:17203
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NCRNA00196
    Expression
    Broad expression in duodenum (RPKM 1.5), gall bladder (RPKM 1.4) and 16 other tissues See more
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    Genomic context

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    See PSORS1C3 in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31173735..31186317, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31041432..31054021, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31141512..31154094, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr6:31127045-31127228 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr6:31128969-31129952 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr6:31129953-31130936 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr6:31132319-31132900 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:31135533-31136390 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:31136391-31137248 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:31137249-31138106 Neighboring gene transcription factor 19 Neighboring gene POU5F1 5' regulatory region Neighboring gene POU class 5 homeobox 1 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31142488-31143384 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31145628-31146222 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31146755-31147256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31148363-31148906 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31153427-31154016 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31154017-31154604 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31158168-31158669 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31163380-31164262 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31166400-31167283 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31167284-31168166 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31169734-31170274 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31170275-31170813 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:31170972-31171692 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:31171693-31172412 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:31172413-31173132 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:31173133-31173851 Neighboring gene HLA complex group 27 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31178749-31179743 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:31180245-31180430 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31183567-31184468 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31190777-31191278 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31192075-31192697 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31192791-31193386 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31196240-31196741 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31197314-31197823 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31203152-31203653 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31207427-31207928 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:31212376-31213125 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31213660-31214161 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31217950-31218451 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31220759-31221378 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31221379-31221998 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31222367-31223043 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31227633-31228239 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31228743-31229244 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31234264-31235207 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31235343-31235902 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31236021-31236522 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:31237308-31237809 Neighboring gene major histocompatibility complex, class I, C

    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 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. Methylomic profiling of cortex samples from completed suicide cases implicates a role for PSORS1C3 in major depression and suicide. Murphy TM, et al. Transl Psychiatry, 2017 Jan 3. PMID 28045465, Free PMC Article
    2. lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells. Mirzadeh Azad F, et al. Sci Rep, 2019 Jun 10. PMID 31182783, Free PMC Article
    3. Novel spliced variants of OCT4, OCT4C and OCT4C1, with distinct expression patterns and functions in pluripotent and tumor cell lines. Malakootian M, et al. Eur J Cell Biol, 2017 Jun. PMID 28476334
    4. Psoriasis vulgaris in Chinese individuals is associated with PSORS1C3 and CDSN genes. Chang YT, et al. Br J Dermatol, 2006 Oct. PMID 16965413
    5. HLA-Cw*0602 associates more strongly to psoriasis in the Swedish population than variants of the novel 6p21.3 gene PSORS1C3. Holm SJ, et al. Acta Derm Venereol, 2005. PMID 15848982

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells.
      Title: lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells.
    2. results show, for the first time, the male-only associations of the PSORS1C3 gene with psoriasis risk and of the PSORS1C1/CDSN gene with severity of disease. However, the age dependent associations need to be validated in larger sample sizes as well as in other populations.
      Title: HLA-C*06:02-independent, gender-related association of PSORS1C3 and PSORS1C1/CDSN single-nucleotide polymorphisms with risk and severity of psoriasis.
    3. Hypomethylation at a differentially methylated region upstream of the PSORS1C3 gene was associated with major depressive disorder suicide cases.
      Title: Methylomic profiling of cortex samples from completed suicide cases implicates a role for PSORS1C3 in major depression and suicide.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Psoriasis vulgaris in Chinese individuals is associated with PSORS1C3 and CDSN genes.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
    EBI GWAS Catalog
    A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients.
    EBI GWAS Catalog
    Genome-wide association study of Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis in Europe.
    EBI GWAS Catalog
    Multiple loci are associated with white blood cell phenotypes.
    EBI GWAS Catalog
    The major genetic determinants of HIV-1 control affect HLA class I peptide presentation.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Potential readthrough

    Included gene: POU5F1

    Other Names

    • psoriasis susceptibility 1 candidate 3 (non-protein coding)

    Clone Names

    • AB023059.1

    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.

    RNA

    1. NR_026816.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC027945

    2. NR_152828.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050981

    3. NR_152829.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050982

    4. NR_152830.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050983

    5. NR_152831.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050984

    6. NR_152832.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050985

    7. NR_152833.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050986

    8. NR_152834.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL662844, LC050987

    9. NR_152835.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050988

    10. NR_152836.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050989

    11. NR_152837.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050990

    12. NR_152838.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC050991

    13. NR_152839.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      LC027946

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      31173735..31186317 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      2656176..2668769 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      2433068..2445657 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      2484255..2496847 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      2517868..2530461 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      2431785..2444362 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      2477166..2489744 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      31041432..31054021 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001134284.1: Suppressed sequence

      Description
      NM_001134284.1: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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