rtcb RNA 2',3'-cyclic phosphate and 5'-OH ligase [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: rtcbprovided by ZNC
Official Full Name: RNA 2',3'-cyclic phosphate and 5'-OH ligaseprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-2096
See related: Ensembl:ENSDARG00000101047 AllianceGenome:ZFIN:ZDB-GENE-040426-2096
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zgc:76871
Summary: Predicted to enable RNA ligase (GTP) activity. Predicted to be involved in tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to act upstream of or within tRNA processing. Predicted to be located in cytoplasm. 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, Jan 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 4

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	4	NC_007115.7 (676710..685412, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	4	NC_007115.6 (663262..671964, complement)

Chromosome 4 - NC_007115.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

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 ZFIN

Function	Evidence Code	Pubs
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables RNA ligase (ATP) activity	IEA Inferred from Electronic Annotation more info
enables RNA ligase (GTP) activity	IEA Inferred from Electronic Annotation more info
enables RNA ligase (GTP) activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA ligase activity	IEA Inferred from Electronic Annotation more info
enables ligase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within RNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within tRNA processing	IEA Inferred from Electronic Annotation more info
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within tRNA splicing, via endonucleolytic cleavage and ligation	IEA Inferred from Electronic Annotation 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	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation 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	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

NP_998268.1

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_213103.1 → NP_998268.1 RNA-splicing ligase RtcB homolog

See identical proteins and their annotated locations for NP_998268.1

Status: PROVISIONAL

Source sequence(s)

BC065987

UniProtKB/Swiss-Prot

Q6NZS4

Related

ENSDARP00000140069.1, ENSDART00000168167.2

Conserved Domains (2) summary

COG1690
Location:28 → 505

RtcB; RNA-splicing ligase RtcB, repairs tRNA damage [Translation, ribosomal structure and biogenesis]

pfam01139
Location:65 → 505

RtcB; tRNA-splicing ligase RtcB