Usb1 U6 snRNA biogenesis phosphodiesterase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Usb1provided by RGD
Official Full Name: U6 snRNA biogenesis phosphodiesterase 1provided by RGD
Primary source: RGD:1305215
See related: Ensembl:ENSRNOG00000013216 AllianceGenome:RGD:1305215
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1305215
Summary: Predicted to enable poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends. Predicted to be involved in RNA splicing and U6 snRNA 3'-end processing. Predicted to be located in intercellular bridge and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in poikiloderma with neutropenia. Orthologous to human USB1 (U6 snRNA biogenesis phosphodiesterase 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 42.7), Lung (RPKM 41.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19p13

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (9695370..9708329, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (9689313..9702306, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (10105750..10118701, complement)

Chromosome 19 - NC_086037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

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General gene information

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Gene Ontology Provided by RGD

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	ISO Inferred from Sequence Orthology more info
enables 3'-5'-RNA exonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables lyase activity	IEA Inferred from Electronic Annotation more info
enables poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends	ISO Inferred from Sequence Orthology more info
enables poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in RNA splicing	ISO Inferred from Sequence Orthology more info
involved_in RNA splicing	ISS Inferred from Sequence or Structural Similarity more info
involved_in U6 snRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in U6 snRNA 3'-end processing	ISO Inferred from Sequence Orthology more info
involved_in U6 snRNA 3'-end processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in snRNA 3'-end processing	ISO Inferred from Sequence Orthology more info
involved_in snRNA 3'-end processing	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in intercellular bridge	IEA Inferred from Electronic Annotation more info
located_in intercellular bridge	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: U6 snRNA phosphodiesterase 1

Names: 3'-5' RNA exonuclease USB1; U6 snRNA biogenesis 1; U6 snRNA phosphodiesterase; UPF0406 protein C16orf57 homolog; putative U6 snRNA phosphodiesterase

NP_001014035.1

EC 3.1.4.-

EC 4.6.1.-

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.