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    NUDT16L1 nudix hydrolase 16 like 1 [ Homo sapiens (human) ]

    Gene ID: 84309, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NUDT16L1provided by HGNC
    Official Full Name
    nudix hydrolase 16 like 1provided by HGNC
    Primary source
    HGNC:HGNC:28154
    See related
    Ensembl:ENSG00000168101 MIM:617338; AllianceGenome:HGNC:28154
    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
    SDOS; TIRR
    Summary
    Enables snoRNA binding activity. Involved in negative regulation of double-strand break repair via nonhomologous end joining. Located in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 5.2), prostate (RPKM 4.4) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See NUDT16L1 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (4693562..4695859)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (4723014..4725311)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (4743563..4745860)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4687274-4688238 Neighboring gene mahogunin ring finger 1 Neighboring gene RNA, 7SL, cytoplasmic 850, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4697151-4697650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4704147-4704648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4704649-4705148 Neighboring gene Sharpr-MPRA regulatory region 2432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4723069-4723658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4723659-4724246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4726242-4726864 Neighboring gene microRNA 6769a Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4732781-4733281 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:4740387-4740751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10343 Neighboring gene hESC enhancers GRCh37_chr16:4743475-4743982 and GRCh37_chr16:4743983-4744490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4745093-4745593 Neighboring gene ankyrin repeat and sterile alpha motif domain containing 3 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr16:4763641-4764282 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr16:4764283-4764922 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:4768049-4768651 and GRCh37_chr16:4768652-4769253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7164 Neighboring gene dynein axonemal assembly factor 8 Neighboring gene zinc finger protein 500

    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. Protein Syndesmos is a novel RNA-binding protein that regulates primary cilia formation. Avolio R, et al. Nucleic Acids Res, 2018 Dec 14. PMID 30260431, Free PMC Article
    2. Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR. Wang J, et al. Nat Commun, 2018 Jul 12. PMID 30002377, Free PMC Article
    3. TIRR inhibits the 53BP1-p53 complex to alter cell-fate programs. Parnandi N, et al. Mol Cell, 2021 Jun 17. PMID 33961797, Free PMC Article
    4. The p53-binding protein 1-Tudor-interacting repair regulator complex participates in the DNA damage response. Zhang A, et al. J Biol Chem, 2017 Apr 21. PMID 28213517, Free PMC Article
    5. Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein. Botuyan MV, et al. Nat Struct Mol Biol, 2018 Jul. PMID 29967538, Free PMC Article

    See all (68) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TIRR inhibits the 53BP1-p53 complex to alter cell-fate programs.
      Title: TIRR inhibits the 53BP1-p53 complex to alter cell-fate programs.
    2. X-ray crystal structures of TIRR and a designer protein bound to 53BP1 now reveal a mechanism in which an intricate binding area centered on an essential TIRR arginine residue blocks the methylated-chromatin-binding surface of 53BP1. A 53BP1 separation-of-function mutation that abolishes TIRR-mediated regulation in cells renders 53BP1 hyperactive in response to DSBs, highlighting the key inhibitory function of TIRR.
      Title: Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein.
    3. Identification of a small subset of mRNAs responsible for the biogenesis of primary cilium that have been linked to developmental and degenerative diseases, known as ciliopathies, and cancer. SDOS binds and regulates the translation of several of these mRNAs, controlling cilia development.
      Title: Protein Syndesmos is a novel RNA-binding protein that regulates primary cilia formation.
    4. This study elucidates the mechanism by which TIRR recognizes 53BP1 Tudor and functions as a cellular inhibitor of the histone methyl-lysine readers.
      Title: Structural basis for recognition of 53BP1 tandem Tudor domain by TIRR.
    5. Data indicate the molecular mechanism underlying Tudor interacting repair regulator (TIRR)-mediated suppression of tumor protein p53 binding protein 1 (53BP1)-dependent DNA damage repair.
      Title: Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR.
    6. findings identify TIRR as a new factor that influences double-strand break repair using a unique mechanism of masking the histone methyl-lysine binding function of 53BP1
      Title: TIRR regulates 53BP1 by masking its histone methyl-lysine binding function.
    7. TIRR is a novel 53BP1-interacting protein that participates in the DNA damage response
      Title: The p53-binding protein 1-Tudor-interacting repair regulator complex participates in the DNA damage response.
    Submit: New GeneRIF Correction

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC11275

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT enables 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA binding HDA PubMed 
    NOT enables phosphodiesterase decapping endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    NOT enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables snoRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables snoRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    NOT involved_in mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in sno(s)RNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tudor-interacting repair regulator protein
    Names
    NUDT16-like protein 1
    nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1
    protein syndesmos
    syndesmos

    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.

    mRNA and Protein(s)

    1. NM_001193452.1 → NP_001180381.1  tudor-interacting repair regulator protein isoform 2

      See identical proteins and their annotated locations for NP_001180381.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC023830, BQ923183, BU739233, DA607298
      Consensus CDS
      CCDS59257.1
      UniProtKB/TrEMBL
      W4VSQ8
      Related
      ENSP00000468346.1, ENST00000586536.1

    2. NM_001370585.1 → NP_001357514.1  tudor-interacting repair regulator protein isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC023830
      UniProtKB/TrEMBL
      B2RD96
      Related
      ENSP00000464821.1, ENST00000590460.1

    3. NM_001370586.1 → NP_001357515.1  tudor-interacting repair regulator protein isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC023830

    4. NM_001370587.1 → NP_001357516.1  tudor-interacting repair regulator protein isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC023830
      Consensus CDS
      CCDS92097.1
      UniProtKB/TrEMBL
      B2RD96, K7ENA3
      Related
      ENSP00000466854.1, ENST00000586252.1

    5. NM_001370588.1 → NP_001357517.1  tudor-interacting repair regulator protein isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC023830

    6. NM_032349.4 → NP_115725.1  tudor-interacting repair regulator protein isoform 1

      See identical proteins and their annotated locations for NP_115725.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC023830
      Consensus CDS
      CCDS10519.1
      UniProtKB/Swiss-Prot
      Q8NAI2, Q9BRJ7
      UniProtKB/TrEMBL
      B2RD96
      Related
      ENSP00000306670.5, ENST00000304301.11

    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
      4693562..4695859
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005255633.6 → XP_005255690.1  tudor-interacting repair regulator protein isoform X1

      Related
      ENSP00000458144.1, ENST00000405142.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      4723014..4725311
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314188.1 → XP_054170163.1  tudor-interacting repair regulator protein isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRJ7.1 GenPept UniProtKB/Swiss-Prot:Q9BRJ7

    Gene LinkOut

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

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