Rtcb RNA 2',3'-cyclic phosphate and 5'-OH ligase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Rtcbprovided by RGD
Official Full Name: RNA 2',3'-cyclic phosphate and 5'-OH ligaseprovided by RGD
Primary source: RGD:1303261
See related: Ensembl:ENSRNOG00000004813 AllianceGenome:RGD:1303261
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable RNA ligase (ATP) activity and vinculin binding activity. Predicted to be involved in tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate. Predicted to act upstream of or within in utero embryonic development and placenta development. Predicted to be located in cytosol; endoplasmic reticulum membrane; and nucleus. Predicted to be part of tRNA-splicing ligase complex. Predicted to be active in nucleus. Orthologous to human RTCB (RNA 2',3'-cyclic phosphate and 5'-OH ligase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 396.1), Liver (RPKM 266.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q13

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (19795393..19814875)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (17907668..17927136)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (23913830..23933191)

Chromosome 7 - NC_086025.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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

What's a GeneRIF?

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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

RH136031 (e-PCR)
- UniSTS:210026

RH129545 (e-PCR)
- UniSTS:212847

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables RNA ligase (ATP) activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA ligase (ATP) activity	IEA Inferred from Electronic Annotation more info
enables RNA ligase (ATP) activity	ISO Inferred from Sequence Orthology more info
enables RNA ligase (ATP) activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA ligase (GTP) activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables vinculin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within placenta development	ISO Inferred from Sequence Orthology more info
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	IEA Inferred from Electronic Annotation more info
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	ISO Inferred from Sequence Orthology more info
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nuclear envelope	ISO Inferred from Sequence Orthology 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
part_of tRNA-splicing ligase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of tRNA-splicing ligase complex	IEA Inferred from Electronic Annotation more info
part_of tRNA-splicing ligase complex	ISO Inferred from Sequence Orthology more info
part_of tRNA-splicing ligase complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: RNA-splicing ligase RtcB homolog

Names: 3'-phosphate/5'-hydroxy nucleic acid ligase; P55; tRNA-splicing ligase RtcB homolog

NP_997497.2

EC 6.5.1.8

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_207614.2 → NP_997497.2 RNA-splicing ligase RtcB homolog

Status: VALIDATED

Source sequence(s)

JAXUCZ010000007

UniProtKB/Swiss-Prot

Q6AYT3, Q6PX76

UniProtKB/TrEMBL

A0A8L2Q3K4, A6IFD0

Related

ENSRNOP00000006570.4, ENSRNOT00000006570.6

Conserved Domains (1) summary

pfam01139
Location:68 → 505

RtcB; tRNA-splicing ligase RtcB