Gene detail

Detailed information of FUN_024110-T1 in Dendrogyra cylindrus

Genomic Location: contig_50:548813...602870
NR annotation: CAH3141791.1, unnamed protein product [Porites lobata]
Species Dendrogyra cylindrus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

FUN_024110-T1

GTACGGCATTGCTTTTCGCTTTcgctgctttttcgctgactcTCGGTCTCTCGCTGACTTTGACTTTGTTGTTTGGAAAAAATTTTTGGACGAGAAATTTAGTTGGAAGTCCTGCAATGGCTCAGCACCGTACGTACAAAGACGAGTGCTCTTTTATTGAGCGCTTAGACAACAATTCCTTTCTTATAAAGAAAGGCTTTGTTCCAAACATGAAGGTTGAGGGTATCTTTTATATCAATGatttacttgaaaagctgatgtTTGATGAACTGAAACACTGGGCTGGGACCCAAGGTATTGGAGGGTTTCTTCCTGGTGTGAAACAGATTGCAAATGTTGCAGCTTTACCTGGCATTGTTGGTAGATCAGTTGGGTTACCAGATGTTCATTCAGGTTATGGATTTGCAATTGGTAATATGGCCGCTTTTGATATGTCACTTCCTGAAGCAGTTGTTTCTCCAGGTGGTGTTGGGTTTGATATCAACTGTGGTGTTAGGCTGTTAAGGACAAACCTTTACGAGAAAGATGTACAGCCTGTTAAAGAACAGCTTGCCCAGTCCCTTTTTGATCACATTCCTGTTGGTGTTGGCTCTAAAGGTGTTATTCCCATGGGAGCAAAAGATTTAGAGGAAGCTCTTTCAATGGGGATGGATTGGTCTCTAAGAGAAGGTTATGCATGGGCTGAAGACAAAGAGCACTGTGAGGAGTATGGACGCATGTTACAGGCTGACCCAGATAAAGTCAGTCCCAGGGCTAAAAAGAGAGGCTTGCCACAGCTTGGTACACTTGGAGCGGGGAATCACTATGCTGAAATCCAGGTTGTTGATGAAATATACAATGAGTATGCTGCAAAGAAGATGGGAGTTGATCATCAGGGACAGGTTTGTGTAATGATCCACAGCGGTAGCAGAGGCCTTGGGCATCAAGTAGCCACTGATGCCCTTGTGGCAATGGAAAAAGCAATGAAAAGAGACAAAATTGATGTAAACGACAGACAGCTTGCATGTGCCAGAATTAACTCACAAGAAGGCCAAGATTATCTCAAGGGCATGGCTGCCGCGGCGAATTATGCCTGGGTTAACCGCTCAACAATGACATTCCTGACAAGACAAGCGTTTGGAAAAGTTTTCAAAAGTACACCAGATGACCTGGACATGCACGTGATCTATGATGTGTCACATAACATTGCCAAGATAGAGGAACATATGTTAGACGGGGAACAGAAGAGCCTACTCGTGCACAGGAAGGGATCAACAAGGGCATTTCCACCTCATCACCCACTTATTCCAGTCGATTATCAGTTGACTGGTCAGCCCGTACTTATAGGAGGAACCATGGGAACCTGTAGTTATGTTCTTACAGGAACAGAGAAAGGAATGAGGCAGACGTTTGGCACAACTTGTCACGGGGCGGGCAGAGCGTTATCGAGAGCAAAGTCGCGGCGAAATCTTGACTATCAGGATGTGCTCGATAGTCTTAAATCCAAAGGAATATCCATCCGAGTGGCTTCTCCCAAGCTCGTCATGGAAGAGgcgCCTGAGTCGTACAAAAACGTCACTGATGTAGTCAATACTTGCCACGATGCAGGAATCAGTCAAAAGGCGATTAAACTAAGACCAATCGCCGTCATCAAAGGATAAACACACGCACGAAATAACAGTTAAATGAAGCTGCAGAACCTATTCTATCTGCGTTTGTGTCCTTCGAAAGTGTTATTTGGTCGTCACGGAATGCTTTTAAGACCTTTTAagggagaagcgttgcgtgacgccAGCGAAGGACAGTACATCCAAGAGAGTCACAAATCTTCCTGTAACGTTTGAGGTTTATAAGAGTTGTTCCTTAGGACCAGCTACATGAGTACTACAAACGTAACAGGGAGTGGCAAAAGTGATATCAGAGAACTCAGATTCCATGTTCAAAACAAATGACTAGGAATCATAACGCACCTAGCTTCCTGAAGAGTGTTCAACATTTACTTCTCTTCATAATGTCAGCACATGTATGTGATTATCCCGAACAACGTTATTTCTATGGttgttttaaacaatttttcccatctagacctaTTAGAAATGTATCAGAatagtaataattattaaataattaatattgtaataaaaaaatgtataatGCTATCATGCCATTCTGCTTTCCAAACAAAGTCATCGTGCTCTGATAAACAACGTGTTATCTGTAACAATAATTTCCGGTTATAAAGTTATGTATGATTTTCATCGAGGTCATCTGATAATCATATTACTTATATTGATATTAATATTGAAATTGATATTGGTGCTGATAACGATTGGAAATCTGTTACTTACTTACCTCTATTAAAAACTGAACTTGTAACAGGGCAGTCCCGAATTCAATGTGTCGTGTCAGACATGTAAAAACTCCTTTCACCTGGTGAAATTTCTAACAAGTTTATGGCAAGTTTGTACTTTACATTTGAGGTCATCATGTATATTTTTTGTGTAATAGTTATTAACCTTTGTTACAGTACATAAATGCGGTTTTTCCAGATAAAGTTTTCTAATCAGGGTATACGATGACTCCAAAAACATCTTGTCTTGCACCGGTGGGCAATAAAACCCTTAGTGTAGAGCTATTTTACACGCTAGTTGTAAATTGATAAATCTTTGTGGCTGAAACGATGGGCTCTAGTGCTGTTTTCTTCACACTTACATTCGTTTTGCTAACAAACGACATTCGAGACAATGGATAGGTTATCATCTTTTGAAATGCGGCGCGAAATCTCTTCTTGAAATATATCAGAAGCCACGGGTTGACTGCACTGTTCGCGTGTCCGCACCAGAAACACACCAACATGACGTAGGAAGGCAGCGACAACGTCAAATTCAGATCGATAGCCAAAATCACGTGATACACATGTGCtggaagccaacaaagtgcaaACGCCACAACGACTGTGATTGACATACGGATGATTTGACGTTTGTTGGCGTTTGCACGGTATGTCGCGCGATTATTGAGGGCAATTCCGGGCAATGTATGCGAGCGGAGTTTTTGACAAACGCAGCCATAGAGAATGCACATTATAGCTAGTGGAAACACGTAGATGGTGAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A7RKF6	RNA-splicing ligase RtcB homolog OS=Nematostella vectensis OX=45351 GN=v1g198406 PE=3 SV=1
Q6NZS4	RNA-splicing ligase RtcB homolog OS=Danio rerio OX=7955 GN=rtcb PE=2 SV=1
Q99LF4	RNA-splicing ligase RtcB homolog OS=Mus musculus OX=10090 GN=Rtcb PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003300 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01139 all species →	RtcB	tRNA-splicing ligase RtcB	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036025 all species →	Homologous_superfamily	tRNA-splicing ligase RtcB-like superfamily	Interproscan
IPR001233 all species →	Family	RNA-splicing ligase, RtcB	Interproscan
IPR027513 all species →	Family	RNA-splicing ligase RtcB homologue, eukaryotic	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11118 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0008452 all species →	Molecular Function	RNA ligase activity	Interproscan
GO:0000971 all species →	Biological Process	obsolete tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate	Interproscan
GO:0003972 all species →	Molecular Function	RNA ligase (ATP) activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0072669 all species →	Cellular Component	tRNA-splicing ligase complex	Interproscan
GO:0006388 all species →	Biological Process	tRNA splicing, via endonucleolytic cleavage and ligation	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14415	RTCB, rtcB; tRNA-splicing ligase RtcB (3'-phosphate/5'-hydroxy nucleic acid ligase)	EC:6.5.1.8	Transfer RNA biogenesis	ko03016	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Dendrogyra cylindrus tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Dendrogyra cylindrus, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →