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    RPH3AL-AS1 RPH3AL antisense RNA 1 [ Homo sapiens (human) ]

    Gene ID: 100506388, updated on 22-Oct-2024

    Summary

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    Official Symbol
    RPH3AL-AS1provided by HGNC
    Official Full Name
    RPH3AL antisense RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:55345
    See related
    Ensembl:ENSG00000262061 AllianceGenome:HGNC:55345
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Biased expression in ovary (RPKM 9.0), adrenal (RPKM 3.0) and 9 other tissues See more
    Orthologs
    all
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    Genomic context

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    See RPH3AL-AS1 in Genome Data Viewer
    Location:
    17p13.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (331519..333488)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (251096..253065)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (181310..183279)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2091 Neighboring gene uncharacterized LOC124903889 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47292 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:69190-69690 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:69691-70191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77137-77637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77764-78286 Neighboring gene rabphilin 3A like (without C2 domains) Neighboring gene ReSE screen-validated silencer GRCh37_chr17:94284-94482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:136075-136596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:150673-151173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:151415-152185 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:152186-152955 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:160317-161015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:161016-161713 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr17:164601-165116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:165117-165633 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:165634-166149 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:166152-166652 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:166653-167153 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:180576-181156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:181157-181735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:183692-184468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:184469-185243 Neighboring gene Sharpr-MPRA regulatory region 15212 Neighboring gene Sharpr-MPRA regulatory region 2375 Neighboring gene uncharacterized LOC105371425 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:216819-218018 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:252557-253756 Neighboring gene uncharacterized LOC105371430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7938 Neighboring gene ligand of ATE1

    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. Generation and analysis of 280,000 human expressed sequence tags. Hillier LD, et al. Genome Res, 1996 Sep. PMID 8889549
    2. 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
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    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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    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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    Markers

    Homology

    Clone Names

    • FLJ30421

    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_040011.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC129507, CB055151, CB055152, DA926752

    2. NR_164141.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC129507
      Related
      ENST00000793093.1

    3. NR_164142.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC129507

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      331519..333488
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315952.3 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      302954..304923
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_187662.1 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      69150..71119 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      251096..253065
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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