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USB1 U6 snRNA biogenesis phosphodiesterase 1 [ Homo sapiens (human) ]

Gene ID: 79650, updated on 5-Mar-2024

Summary

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Official Symbol
USB1provided by HGNC
Official Full Name
U6 snRNA biogenesis phosphodiesterase 1provided by HGNC
Primary source
HGNC:HGNC:25792
See related
Ensembl:ENSG00000103005 MIM:613276; AllianceGenome:HGNC:25792
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
PN; Mpn1; HVSL1; hMpn1; hUsb1; C16orf57
Summary
This gene encodes a protein with several conserved domains, however, its exact function is not known. Mutations in this gene are associated with poikiloderma with neutropenia (PN), which shows phenotypic overlap with Rothmund-Thomson syndrome (RTS) caused by mutations in the RECQL4 gene. It is believed that this gene product interacts with RECQL4 protein via SMAD4 proteins, explaining the partial clinical overlap between PN and RTS. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in appendix (RPKM 7.3), bone marrow (RPKM 6.0) and 25 other tissues See more
Orthologs
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Genomic context

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See USB1 in Genome Data Viewer
Location:
16q21
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (57999603..58021618)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (63794892..63816894)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (58033507..58055522)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57917491-57918038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57918039-57918586 Neighboring gene cyclic nucleotide gated channel subunit beta 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57945302-57946008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57972707-57973534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57973535-57974362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57998489-57998988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10918 Neighboring gene sperm microtubule inner protein 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43822 Neighboring gene Sharpr-MPRA regulatory region 3942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10920 Neighboring gene zinc finger protein 319 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:58046115-58046647 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:58046648-58047179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58058267-58058854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58058855-58059440 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:58059673-58060222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58060773-58061322 Neighboring gene matrix metallopeptidase 15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:58119688-58120378 Neighboring gene TIPIN pseudogene 2

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. USB1 is a miRNA deadenylase that regulates hematopoietic development. Jeong HC, et al. Science, 2023 Mar 3. PMID 36862787, Free PMC Article
  2. Kindler epidermolysis bullosa-like skin phenotype and downregulated basement membrane zone gene expression in poikiloderma with neutropenia and a homozygous USB1 mutation. Vahidnezhad H, et al. Matrix Biol, 2021 May. PMID 34004352
  3. Clinical Sequencing Solves a Diagnostic Dilemma by Identifying a Novel Pathogenic Variant in USB1 Gene Causing Poikiloderma with Neutropenia. Gangadharan H, et al. Indian J Pediatr, 2021 Mar. PMID 32936385
  4. Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1. Nomura Y, et al. Nucleic Acids Res, 2018 Nov 30. PMID 30215753, Free PMC Article
  5. Poikiloderma with neutropenia in a Tunisian patient with a novel C16orf57 gene mutation. Sakka R, et al. Pediatr Blood Cancer, 2018 Sep. PMID 29797650

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Defective monocyte plasticity and altered cAMP pathway characterize USB1-mutated poikiloderma with neutropenia Clericuzio type.
    Title: Defective monocyte plasticity and altered cAMP pathway characterize USB1-mutated poikiloderma with neutropenia Clericuzio type.
  2. Chinese nontwin sisters suffer from poikiloderma with neutropenia harboring novel compound heterozygous USB1 gene mutations.
    Title: Chinese nontwin sisters suffer from poikiloderma with neutropenia harboring novel compound heterozygous USB1 gene mutations.
  3. USB1 is a miRNA deadenylase that regulates hematopoietic development.
    Title: USB1 is a miRNA deadenylase that regulates hematopoietic development.
  4. Kindler epidermolysis bullosa-like skin phenotype and downregulated basement membrane zone gene expression in poikiloderma with neutropenia and a homozygous USB1 mutation.
    Title: Kindler epidermolysis bullosa-like skin phenotype and downregulated basement membrane zone gene expression in poikiloderma with neutropenia and a homozygous USB1 mutation.
  5. Clinical Sequencing Solves a Diagnostic Dilemma by Identifying a Novel Pathogenic Variant in USB1 Gene Causing Poikiloderma with Neutropenia.
    Title: Clinical Sequencing Solves a Diagnostic Dilemma by Identifying a Novel Pathogenic Variant in USB1 Gene Causing Poikiloderma with Neutropenia.
  6. Clericuzio-type poikiloderma with neutropenia in a patient from India.
    Title: Clericuzio-type poikiloderma with neutropenia in a patient from India.
  7. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively
    Title: Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.
  8. Data show that U6 snRNA phosphodiesterase (Usb1) removes 3' adenosines with 20-fold greater efficiency than uridines.
    Title: Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1.
  9. A novel homozygous deletion of a 1-bp (c.161delC, p.P54RfsX60) in the C16orf57gene, was presumed to be causative of poikiloderma with neutropenia. The patient's asymptomatic consanguineous parents were heterozygotes for this mutation.
    Title: Poikiloderma with neutropenia in a Tunisian patient with a novel C16orf57 gene mutation.
  10. this paper describes USB1 mutations characterized in four Moroccan patients out of three unrelated consanguinous families
    Title: Poikiloderma with Neutropenia in Morocco: a Report of Four Cases.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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
Poikiloderma with neutropenia
MedGen: C1858723 OMIM: 604173 GeneReviews: Poikiloderma with Neutropenia
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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

  • FLJ13154

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5'-RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 3'-5'-RNA exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables lyase activity IEA
Inferred from Electronic Annotation
more info
  
enables poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA splicing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in U6 snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in U6 snRNA 3'-end processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in U6 snRNA 3'-end processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in snRNA 3'-end processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in intercellular bridge IDA
Inferred from Direct Assay
more info
  
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
U6 snRNA phosphodiesterase 1
Names
3'-5' RNA exonuclease USB1
HVSL motif containing 1
U six biogenesis 1
U6 snRNA biogenesis 1
U6 snRNA phosphodiesterase
UPF0406 protein C16orf57
mutated in PN protein 1
mutated in poikiloderma with neutropenia protein 1
putative U6 snRNA phosphodiesterase
NP_001182231.1
NP_001191840.1
NP_001317497.1
NP_001317498.1
NP_078874.2

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_027698.1 RefSeqGene

    Range
    5001..25251
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_352

mRNA and Protein(s)

  1. NM_001195302.2 → NP_001182231.1  U6 snRNA phosphodiesterase 1 isoform 2

    See identical proteins and their annotated locations for NP_001182231.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AC012182, AK303121, DB364698, DC363309
    Consensus CDS
    CCDS55998.1
    UniProtKB/TrEMBL
    H3BTT8
    Related
    ENSP00000446143.2, ENST00000539737.6
    Conserved Domains (1) summary
    pfam09749
    Location:44 → 245
    HVSL; uncharacterized conserved protein

  2. NM_001204911.2 → NP_001191840.1  U6 snRNA phosphodiesterase 1 isoform 3

    See identical proteins and their annotated locations for NP_001191840.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks several exons from the 3' end, and contains an alternate 3' terminal exon compared to variant 1. This results in a shorter isofom (3) with a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC010543, AK301494, BF733890, BI910866, BQ223186, BX117268, DB382938, DC380401
    Consensus CDS
    CCDS55997.1
    UniProtKB/TrEMBL
    A0A8V8TLQ0
    Related
    ENSP00000409792.3, ENST00000423271.8
    Conserved Domains (1) summary
    pfam09749
    Location:44 → 151
    HVSL; uncharacterized conserved protein

  3. NM_001330568.2 → NP_001317497.1  U6 snRNA phosphodiesterase 1 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate 5' terminal exon, resulting in a distinct 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC012182, BC007774, DC386004
    Consensus CDS
    CCDS81991.1
    UniProtKB/TrEMBL
    H3BNM8, H3BTT8
    Related
    ENSP00000454928.1, ENST00000561743.5
    Conserved Domains (1) summary
    pfam09749
    Location:1 → 212
    HVSL; uncharacterized conserved protein

  4. NM_001330569.2 → NP_001317498.1  U6 snRNA phosphodiesterase 1 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks several exons in the 3' coding region, and includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC010543
    Consensus CDS
    CCDS81990.1
    UniProtKB/TrEMBL
    A0A8V8TNL4, H3BN52
    Related
    ENSP00000454692.1, ENST00000563149.2
    Conserved Domains (1) summary
    pfam09749
    Location:44 → 149
    HVSL; uncharacterized conserved protein

  5. NM_024598.4 → NP_078874.2  U6 snRNA phosphodiesterase 1 isoform 1

    See identical proteins and their annotated locations for NP_078874.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC012182, BC004415, DB364698, DC363309
    Consensus CDS
    CCDS10791.1
    UniProtKB/Swiss-Prot
    B4DWE3, B4DZW5, Q96FZ9, Q9BQ65, Q9H8X8
    UniProtKB/TrEMBL
    H3BTT8
    Related
    ENSP00000219281.3, ENST00000219281.8
    Conserved Domains (1) summary
    pfam09749
    Location:44 → 263
    HVSL; Uncharacterized conserved protein

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
    57999603..58021618
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    63794892..63816894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BQ65.1 GenPept UniProtKB/Swiss-Prot:Q9BQ65

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