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Rtcb RNA 2',3'-cyclic phosphate and 5'-OH ligase [ Mus musculus (house mouse) ]

Gene ID: 28088, updated on 12-May-2024

Summary

Official Symbol
Rtcbprovided by MGI
Official Full Name
RNA 2',3'-cyclic phosphate and 5'-OH ligaseprovided by MGI
Primary source
MGI:MGI:106379
See related
Ensembl:ENSMUSG00000001783 AllianceGenome:MGI:106379
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
FAAP; HSPC117; D10Wsu52e
Summary
Predicted to enable RNA ligase (ATP) activity and vinculin binding activity. Acts upstream of or within in utero embryonic development and placenta development. Located in endoplasmic reticulum membrane and nuclear envelope. Is expressed in several structures, including early conceptus and placenta. Orthologous to human RTCB (RNA 2',3'-cyclic phosphate and 5'-OH ligase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in genital fat pad adult (RPKM 77.2), CNS E11.5 (RPKM 72.6) and 28 other tissues See more
Orthologs
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Genomic context

See Rtcb in Genome Data Viewer
Location:
10 C1; 10 41.81 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (85774501..85793657, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (85938637..85957793, complement)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene PR domain containing 4 Neighboring gene STARR-positive B cell enhancer ABC_E723 Neighboring gene achaete-scute family bHLH transcription factor 4 Neighboring gene STARR-seq mESC enhancer starr_27454 Neighboring gene STARR-positive B cell enhancer ABC_E11450 Neighboring gene predicted gene, 48175 Neighboring gene BPI fold containing family C Neighboring gene STARR-seq mESC enhancer starr_27455 Neighboring gene STARR-positive B cell enhancer ABC_E8355 Neighboring gene F-box protein 7 Neighboring gene predicted gene, 24430

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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 ISO
Inferred from Sequence Orthology
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
 
enables vinculin binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in RNA processing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within in utero embryonic development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within placenta development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within tRNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in tRNA splicing, via endonucleolytic cleavage and ligation ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
 
located_in nuclear envelope IDA
Inferred from Direct Assay
more info
PubMed 
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
 
part_of tRNA-splicing ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of tRNA-splicing ligase complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
RNA-splicing ligase RtcB homolog
Names
3'-phosphate/5'-hydroxy nucleic acid ligase
focal adhesion-associated protein
tRNA-splicing ligase RtcB homolog
NP_663397.1

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.

mRNA and Protein(s)

  1. NM_145422.4NP_663397.1  RNA-splicing ligase RtcB homolog

    See identical proteins and their annotated locations for NP_663397.1

    Status: PROVISIONAL

    Source sequence(s)
    AC122919, AC151901
    Consensus CDS
    CCDS24094.1
    UniProtKB/Swiss-Prot
    Q3TA04, Q3TI25, Q3UDW6, Q99LF4
    UniProtKB/TrEMBL
    Q3TJ01
    Related
    ENSMUSP00000001834.4, ENSMUST00000001834.4
    Conserved Domains (1) summary
    pfam01139
    Location:68505
    RtcB; tRNA-splicing ligase RtcB

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    85774501..85793657 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)