DBR1 debranching RNA lariats 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DBR1provided by HGNC
Official Full Name: debranching RNA lariats 1provided by HGNC
Primary source: HGNC:HGNC:15594
See related: Ensembl:ENSG00000138231 MIM:607024; AllianceGenome:HGNC:15594
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: XGIP
Summary: The protein encoded by this gene is an RNA lariat debranching enzyme that hydrolyzes 2'-5' prime branched phosphodiester bonds. The encoded protein specifically targets the bonds at the branch point of excised lariat intron RNA, converting them to linear molecules that are then degraded. This protein may also be involved in retroviral replication. [provided by RefSeq, Nov 2011]
Expression: Ubiquitous expression in stomach (RPKM 5.7), bone marrow (RPKM 5.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q22.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (138160988..138174921, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (140901580..140915511, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (137879830..137893763, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Trichothiodystrophy-associated MPLKIP maintains DBR1 levels for proper lariat debranching and ectodermal differentiation.
Title: Trichothiodystrophy-associated MPLKIP maintains DBR1 levels for proper lariat debranching and ectodermal differentiation.
A founder DBR1 variant causes a lethal form of congenital ichthyosis.
Title: A founder DBR1 variant causes a lethal form of congenital ichthyosis.
Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product.
Title: Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product.
The Role of DBR1 as a Candidate Prognosis Biomarker in Esophageal Squamous Cell Carcinoma.
Title: The Role of DBR1 as a Candidate Prognosis Biomarker in Esophageal Squamous Cell Carcinoma.
findings support a new view of the early steps in HIV genome replication - they support a model in which lariat formation of viral genomic RNA is important for minus-strand transfer, with DBR1 being required to resolve the lariat to allow reverse transcription to proceed
Title: Conformational Changes in the 5' End of the HIV-1 Genome Dependent on the Debranching Enzyme DBR1 during Early Stages of Infection.
Transcriptomic sequencing confirmed the effect of hDBR1 on RNA splicing, and metabolite profiling supported the observation that neoplasm is triggered by a decrease in hDBR1 expression both in vitro and in vivo.
Title: Human DBR1 modulates the recycling of snRNPs to affect alternative RNA splicing and contributes to the suppression of cancer development.
saturation mutagenesis of DBR1 and Gal4 and show that the experimental phenotypes for over 80% of the mutations correlate well with predicted effects of mutations on protein stability and RNA binding affinity.
Title: In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity.
Results of protein-protein interaction between human Dbr1 and factors found in the Intron Large complex identify Xab2 and a novel protein CWF19L1 as specific interactors of DBR1.
Title: Identification of the specific interactors of the human lariat RNA debranching enzyme 1 protein.
Inhibition of DBR1 caused a significant reduction in the formation of intermediate and full-length HIV-1 cDNA.
Title: Impairment of HIV-1 cDNA synthesis by DBR1 knockdown.
Dbr1 protein cleaves the 2'-5' phosphodiester bond of intron lariats, necessary for subsequent intron degradation that follows pre-mRNA splicing.
Title: Isolation and characterization of the gene encoding yeast debranching enzyme.

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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

Associated conditions

Description	Tests
Encephalitis, acute, infection (viral)-induced, susceptibility to, 11 MedGen: C5561941 OMIM: 619441 GeneReviews: Not available	Compare labs
Xerosis and growth failure with immune and pulmonary dysfunction syndrome MedGen: CN374328 OMIM: 620510 GeneReviews: Not available	not available

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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA lariat debranching enzyme activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA lariat debranching enzyme activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in RNA fragment catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA splicing, via transesterification reactions	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleoplasm	IDA Inferred from Direct Assay more info
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: lariat debranching enzyme

Names: RNA lariat debranching enzyme; debranching enzyme homolog 1

NP_057300.2

EC 3.1.4.-

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)

NM_016216.4 → NP_057300.2 lariat debranching enzyme

See identical proteins and their annotated locations for NP_057300.2

Status: REVIEWED

Source sequence(s)

AC023049, AL702928, BC009472, BF987317, CD677175

Consensus CDS

CCDS33863.1

UniProtKB/Swiss-Prot

Q96GH0, Q9NXQ6, Q9UK59

UniProtKB/TrEMBL

A0A8V8TNX0

Related

ENSP00000260803.4, ENST00000260803.9

Conserved Domains (2) summary

cd00844
Location:3 → 264

MPP_Dbr1_N; Dbr1 RNA lariat debranching enzyme, N-terminal metallophosphatase domain

pfam05011
Location:246 → 379

DBR1; Lariat debranching enzyme, C-terminal domain