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    LOC100420587 SHC binding and spindle associated 1 pseudogene [ Homo sapiens (human) ]

    Gene ID: 100420587, updated on 22-Oct-2024

    Summary

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    Gene symbol
    LOC100420587
    Gene description
    SHC binding and spindle associated 1 pseudogene
    See related
    Ensembl:ENSG00000290606
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LOC100420587 in Genome Data Viewer
    Location:
    19q12
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (28435388..28727694, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (30965335..31257653, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (28926295..29218601, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2987 Neighboring gene uncharacterized LOC105372347 Neighboring gene uncharacterized LOC105372346 Neighboring gene zinc finger protein 709 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14404 Neighboring gene NANOG hESC enhancer GRCh37_chr19:28621443-28621988 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:28659458-28660167 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:28660168-28660878 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:28726469-28727180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:28727181-28727891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:28760939-28761439 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:28781600-28782131 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr19:28794338-28794874 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:28804274-28805473 Neighboring gene MPRA-validated peak3419 silencer Neighboring gene MPRA-validated peak3420 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:28881947-28882183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:28890814-28891468 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:28891469-28892122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:28893490-28894450 Neighboring gene MPRA-validated peak3422 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:28913828-28914513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:28917241-28917759 Neighboring gene Sharpr-MPRA regulatory region 924 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:28916721-28917240 Neighboring gene uncharacterized LOC105372349 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:28936697-28937404 Neighboring gene Sharpr-MPRA regulatory region 12624 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:29036304-29036510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:29080318-29080960 Neighboring gene uncharacterized LOC124904681 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:29096818-29098017 Neighboring gene Sharpr-MPRA regulatory region 736 Neighboring gene Sharpr-MPRA regulatory region 5210 Neighboring gene uncharacterized LOC124904679 Neighboring gene endogenous retrovirus group E member 5 Neighboring gene MPRA-validated peak3425 silencer Neighboring gene mannosidase alpha class 1A member 2 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:29371723-29372474 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:29372475-29373224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:29373975-29374724 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:29395574-29395771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29402081-29402580 Neighboring gene small nucleolar RNA U13

    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. Bivariate genome-wide association analyses identified genes with pleiotropic effects for femoral neck bone geometry and age at menarche. Ran S, et al. PLoS One, 2013. PMID 23593202, Free PMC Article
    2. Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan. Low SK, et al. Cancer Sci, 2013 Aug. PMID 23648065, Free PMC Article
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Bivariate genome-wide association analyses identified genes with pleiotropic effects for femoral neck bone geometry and age at menarche.
    EBI GWAS Catalog
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    EBI GWAS Catalog

    Variation

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    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    General gene information

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    Clone Names

    • AC005307.3

    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_110759.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC068609, DB120589, HY016521
      Related
      ENST00000592347.5

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      28435388..28727694 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      30965335..31257653 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_024175.1: Suppressed sequence

      Description
      NG_024175.1: This RefSeq was permanently suppressed because it is now thought that this is a transcribed pseudogene.
    Nucleotide Protein
    Heading Accession and Version

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