U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

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

Summary

Go to the top of the page Help
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
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

NEW Try the new Transcript table

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools