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

Gene ID: 113000, updated on 5-Mar-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, Apr 2022]
Expression
Ubiquitous expression in spleen (RPKM 5.2), colon (RPKM 4.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16p13.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (784974..788381, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (789685..793092, complement)
105.20220307 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)

Genotypes

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 molecular_function ND
No biological Data available
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 biological_process ND
No biological Data available
more info
  
involved_in enzyme-directed rRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
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_2023_10

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

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