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    RPUSD1 RNA pseudouridine synthase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 113000, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RPUSD1provided by HGNC
    Official Full Name
    RNA pseudouridine synthase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:14173
    See related
    Ensembl:ENSG00000007376 AllianceGenome:HGNC:14173
    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
    RLUCL; C16orf40
    Summary
    Predicted to enable pseudouridine synthase activity. Predicted to be involved in enzyme-directed rRNA pseudouridine synthesis. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 5.2), colon (RPKM 4.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RPUSD1 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (784974..788381, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (789685..793092, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (834974..838381, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene MSLN promoter region Neighboring gene mesothelin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:836847-837654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6957 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6958 Neighboring gene microRNA 662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6959 Neighboring gene mesothelin like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:844412-845141 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46330 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:850423-850972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:850973-851522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:851523-852072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:852890-853434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:853979-854522 Neighboring gene chromosome transmission fidelity factor 18 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6961 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:867140-867640 Neighboring gene G protein subunit gamma 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:890022-890522 Neighboring gene lipase maturation factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:935837-936415 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:936416-936993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:940581-941424 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:946091-946310 Neighboring gene peptidyl-prolyl cis-trans isomerase CYP95-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:951356-952074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:952075-952792 Neighboring gene uncharacterized LOC107984876

    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. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. Daniels RJ, et al. Hum Mol Genet, 2001 Feb 15. PMID 11157797
    2. Transcriptome analysis of human gastric cancer. Oh JH, et al. Mamm Genome, 2005 Dec. PMID 16341674
    3. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Antoniali G, et al. Nat Commun, 2017 Oct 6. PMID 28986522, Free PMC Article
    4. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Brandenberger R, et al. Nat Biotechnol, 2004 Jun. PMID 15146197
    5. UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Liu J, et al. Nat Cell Biol, 2020 Sep. PMID 32807901

    See all (12) citations in PubMed

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC19600

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pseudouridine synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in enzyme-directed rRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RNA pseudouridylate synthase domain-containing protein 1
    Names
    RNA pseudouridylate synthase domain containing 1
    ribosomal large subunit pseudouridine synthase C-like 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.

    Genomic

    1. NG_047098.1 RefSeqGene

      Range
      5007..8414
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001324086.2 → NP_001311015.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL031033
      Conserved Domains (2) summary
      cd02869
      Location:18 → 218
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family
      COG0564
      Location:9 → 233
      RluA; Pseudouridylate synthase, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]

    2. NM_001324410.2 → NP_001311339.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL031033, AL514840
      UniProtKB/TrEMBL
      H3BMZ6
      Related
      ENSP00000454616.1, ENST00000569601.5
      Conserved Domains (1) summary
      cd02869
      Location:9 → 89
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    3. NM_001324411.2 → NP_001311340.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL031033, AL520203
      Consensus CDS
      CCDS81924.1
      UniProtKB/TrEMBL
      H3BUN6
      Related
      ENSP00000457722.1, ENST00000565809.5
      Conserved Domains (1) summary
      cd02869
      Location:18 → 103
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    4. NM_001324412.2 → NP_001311341.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5), as well as variants 6, 7, and 8, encodes isoform 5.
      Source sequence(s)
      AL031033, BX358716
      Consensus CDS
      CCDS81923.1
      UniProtKB/TrEMBL
      H3BMZ6, H3BQN8
      Related
      ENSP00000455862.1, ENST00000567114.5
      Conserved Domains (1) summary
      cd02869
      Location:8 → 86
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    5. NM_001324413.2 → NP_001311342.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6), as well as variants 5, 7, and 8, encodes isoform 5.
      Source sequence(s)
      AL031033, CN311779
      Consensus CDS
      CCDS81923.1
      UniProtKB/TrEMBL
      H3BMZ6, H3BQN8
      Related
      ENSP00000456692.1, ENST00000565377.1
      Conserved Domains (1) summary
      cd02869
      Location:8 → 86
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    6. NM_001324414.2 → NP_001311343.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7), as well as variants 5, 6, and 8, encodes isoform 5.
      Source sequence(s)
      AL031033, CN311777
      Consensus CDS
      CCDS81923.1
      UniProtKB/TrEMBL
      H3BMZ6, H3BQN8
      Conserved Domains (1) summary
      cd02869
      Location:8 → 86
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    7. NM_001324415.2 → NP_001311344.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variants 5, 6, and 7, encodes isoform 5.
      Source sequence(s)
      AL031033, CX786721
      Consensus CDS
      CCDS81923.1
      UniProtKB/TrEMBL
      H3BMZ6, H3BQN8
      Conserved Domains (1) summary
      cd02869
      Location:8 → 86
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    8. NM_001369658.1 → NP_001356587.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL031033
      Conserved Domains (1) summary
      cd02869
      Location:18 → 199
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    9. NM_001369659.1 → NP_001356588.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL031033
      UniProtKB/TrEMBL
      H3BMZ6
      Conserved Domains (1) summary
      cd02869
      Location:9 → 89
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    10. NM_001369660.1 → NP_001356589.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL031033
      Consensus CDS
      CCDS81923.1
      UniProtKB/TrEMBL
      H3BMZ6, H3BQN8
      Conserved Domains (1) summary
      cd02869
      Location:8 → 86
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family

    11. NM_058192.3 → NP_478072.1  RNA pseudouridylate synthase domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_478072.1

      Status: VALIDATED

      Source sequence(s)
      BC011783, BG686882, BM763460, CB529100
      Consensus CDS
      CCDS10426.1
      UniProtKB/Swiss-Prot
      D3DU66, Q9UJJ7
      Related
      ENSP00000007264.2, ENST00000007264.7
      Conserved Domains (2) summary
      cd02869
      Location:18 → 215
      PseudoU_synth_RluCD_like; Pseudouridine synthase, RsuA/RluD family
      COG0564
      Location:9 → 230
      RluA; Pseudouridylate synthase, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      784974..788381 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      789685..793092 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UJJ7.1 GenPept UniProtKB/Swiss-Prot:Q9UJJ7

    Gene LinkOut

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

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