Gene detail

Detailed information of FUN_007751-T1 in Dendrogyra cylindrus

Genomic Location: contig_9:3155762...3169392
NR annotation: XP_020601267.1, threonylcarbamoyladenosine tRNA methylthiotransferase-like [Orbicella faveolata]
Species Dendrogyra cylindrus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

FUN_007751-T1

ACAGCATGGCGCAACAACATGGCGGCCTGGCAGTAGCAGTGTGATCAATTTTCTTACGCTTCGGGGAGGAATAAATGTTCTTTGCCTCAAGATATCATGTGAAACTGTAAAGCGTTGACAAGGAGAAAACTTTTTTGATTAACTTTGGTGTTCAAGCGGCTACAGTcaatAATCTGTTCATGTTCAACCAAAAAATGCCGTCCTGTGATTTGGAAGTATGTGACATTGAAGATGCTGTGAGGAAGGATGATCTCACGCCTAATGACCGCATCACGCCTCGGGACTCTGTCGTTCCAAAAGCAAGAGTAAGATCCAAGCGGAATGTAGTGAGTGAGCCCCCAGTAGGTGACAGTGTTATCCCCGGCACACAGAAGATTTATGTTAGAACTTGGGGATGTTCCCATAATAACAGTGATGGTGAATATATGGCAGGGCAACTGGCAGCCTTTGGTTATAAAATTACAGATGACTCAGAAGCAGCTGATCTGTGGCTTCTTAACAGCTGCACAGTGAAGAACCCTTCAGAAGATAACTTTAGAAATGCAATCAAAAGAGCACAGGAACTTGATAAACACTTGGTCGTTGCAGGCTGTGTACCGCAAGGACAACCCAAACACCAGTCGATCAAAGGGATCAGTGTGATAGGGGTGCAGCAAATTGACAGAGTGGTGGAAGTTGTAGAGGAAACTTTAAAAGGTCACACAGTTCGACTTCTTGGTCAAAAGAAAGTTGCTGGAAAGAAAGCTGGGGGAGCTCCACTTGATTTACCTAAAATTCGGAAAAATCCTCTGATAGAAATTATAGCAATAAATACTGGGTGTCTAAACCAGTGCACTTACTGCAAGACAAAGCATGCTCGAGGAGATCTGGGAAGTTATCCACCTGAAGAGATTGTTGCGAGAGCCAAGCAAGCCTTTGAAGAGGGAGTTGTTGAGCTGTGGCTGACAAGTGAAGACACAGGAGCATACGGAAGAGACATTGGCGTCACATTACCtgagttgctatggcaacttGTGGAGGTGATTCCAGAAGGAGCCATGATGAGGATTGGAATGACAAACCCACCATACATCCTGGAACACTTGGAGGAAATGGCCAAAATCCTAAACCATCCTCGAGTTTACAGTTTTCTTCATGTACCAGTTCAAAGTGCATCAGACAATGTGCTTGGCGACATGAAAAGAGAGtactgtgctgatgattttagACATGTTGTGGACTTTCTAAAAGACAAGGTACCAGGAATCACCATAGCAACAGATGTAATCTGCGGCTTCCCAACAGAGACCTGGGAAGACTTTCAGGAAACAGTAGCATTGGTGGAGCAGTATAAATTTCCCAGCCTGTTTATCAATCAGTTCTATCCACGCCCAGGGACCCCTGCTGCGAGAATGAAGAGACACCCCACAGAAGAGGTTAAGAAGCGAACAAGGGAGATTTCTAAACTATTTCATAGCTACCACCCTTATGATCATAAGGTTGGCGAGAGGCAAACTGTCCTAATAACAGAAGACGCGAAGGACCAAGCTCATTTCGTTGGCCACAATAAGTATTATGATCAAGTCCTTATTCACAAGAGTGAAGGCAACCTCATGGGTAAAATGGTCCAAGTAGAAATAACATCAGCTGGAGAACACTTTCAAATGGCGCGTGTCTTGCGTGATAGTGAGGCTCATTCACCCGGCCTGGTTGAGCCGCTACCAAAAGGTGCGGTCAGTGGTGTTCGTACAAAGCCCACGCACGAAAGCACTGTTCACAATCAAGAAAGCCCTTGGAACCAGTGGACAAAAGCTGCTGTGGTTGTCCTACTAGCAGTTGTCTTAGTCGATGTTTTAAGACTTTTGTATTTATGGAGCAGCCAGTAAAATTgtgaaaatatattatatctcTAAGCGAGAGCTTGAACTGTGTCGTATCAGGAGCCTGCAATCGCAGCCAAACCCTGTTGAGAATACAAGCATTTTCGGCAAACTTTTCACTCATTTCAAGAAGTATACATTTCCTACTTGGAATTCTTGCCCTCCCCACTCCCCACCCTCCCCACTTCCCACCCTCCCCACTTCCCACCCTCCCCACTTCCCGCCCTCCCCCCCGCCCCCCGCCCCCACCCTGGCCCAATGTTTAGTGTTTGTTTCTAGAAATGTTTGTAGCCAGAAACCCACCGGAAACAACATTGtatggaggggggagggggagggggctgAGATATGCTCCCTAGGTGGATGCAGTGTAAAATTGGGGTATGTGTCTCAACAGTTGCGACCGAGATTGTGGGTTACTGGTCGTATGTAGTTTTAATGCAATAAAAGAACACTCATTTTGTTCTTATTTATCTTTCTTtgagggaggcgcggtggcctagtggttaaaAGGTCATTAAGCGATTAGACGATTGAACACCTGAAACAGGCTACCACGGGACTagcatcatttttttttcgctgaaATATGAAGTTTGCATGatttatttatatatacaaAAGATTATGTGGAAACACAGTAAATGATAACGGGAAAATTCAGTGCAGGAAATTTTACTGGAAGTGAGGTTTTCACGAAGTATATTTTGGAGCAATAGAtgcatttttaaatatatatataacttaGAACGAAATTGTACATGTTTCATAAAATTTGAAAGGGGaccgaaaaaaaaatgatttcaacGAGTCAAGTTTCTAGAAAATCAGTAAGTGCGATCACTCCAGTTTTTCGTActcttgattaaaaaaaaaatgcatatcTTCACCGGAATCAAAGGAAAACGCCGACACTGTTTTTTAGTGGCGTTGAGGGGATTGCGCTATAGCGCCAGAGAGGTGCTTCAGGCGTTCCCACAGAAATTCGCAAATACACACGAAATGGAAAGTGATCTATGATATAATCCAGACACGCTGCTTCTATTATATTCTGAAAACACAGTGAAGATACGAAAAACAGAACGCAGCTCCTTCAGTCATTTTCCTGCGTTTAGAaagtatttttgttgttgtagaacgtttaaaataatctgaaaaagaaaaaaaaaaaaaaggctgcaAAAATGCCGGGACCAGGATTCGAACCTGGGTTACTGCGGCCACAACGCAGTGTCCTAACCACTAGACGATCGCGGCGAGCCACCGAGGAGGTGGTTGAGAAGGTAGGTAATTATTACAATTAAAATGCGCAGCAGGTGTTACACTGACGGTGCGTGCCCTCGTTGTCACACCCATGCAAAGTATGTAAGATGGCCGCTTACGGAAGAAAAAGTTAAGTCTGGCTTCAGGCTACCCTGGGGCACTTTGTCAGTGTGTTCCTTTTCCGCGCGCTACAAGCCTTTGTCCACTCGTCGACACTCGTCCCCAACGCCCGCGATCAATTTGGACTGCGCCAAGGATCCAGACCTCTTACCGCTTCCAAagccggaagtccgcgattcaccggctcattgtcaaatctgagaAATCTGATTGCCTGAAAATACAGAACCAGTACGCTGCGCATGCTCAAAAATTGGGTGCGGCCGGAGATCTCGATCCTTGGCGGAGTACAAATGACTcgcgcggcctctgggaacgagaatggacTTTGCCTTGTAAATACCTCATTACATTAAATTTTTGCGACACGTTGATTTCGTGAatttcgtgattttttttttaagttatgcgAACAATAATTGTCGCCAGAAGTTCATAAGCCGGAAGTCTACATCTAGTTTCTGGGCACGTGCTATTTCTTTCGCGAGGCTATTTGAAGAAACGttgctcgcgagaaaatgacgtatttTGTGGCGTGCAGGTGCAATCGGATGTTGCAAACTACGGCCTTCGGTTGCGGTCTTAATTGGTTTGTGGGTCCTTCATTTTGGCGGACcatgaaaagaaaattttatagAAGAACCACTAGAAGCGAATTTTTCGTCACCATCAGCTCGAAGC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6NS26	Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Xenopus laevis OX=8355 GN=cdkal1 PE=2 SV=1
Q6P4Y0	Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Xenopus tropicalis OX=8364 GN=cdkal1 PE=2 SV=1
Q5VV42	Threonylcarbamoyladenosine tRNA methylthiotransferase OS=Homo sapiens OX=9606 GN=CDKAL1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005693 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01938 all species →	TRAM	TRAM domain	Domain	Interproscan
PF00919 all species →	UPF0004	Uncharacterized protein family UPF0004	Family	Interproscan
PF04055 all species →	Radical_SAM	Radical SAM superfamily	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR023404 all species →	Homologous_superfamily	Radical SAM, alpha/beta horseshoe	Interproscan
IPR002792 all species →	Domain	TRAM domain	Interproscan
IPR020612 all species →	Conserved_site	Methylthiotransferase, conserved site	Interproscan
IPR007197 all species →	Domain	Radical SAM	Interproscan
IPR006466 all species →	Family	MiaB-like tRNA modifying enzyme, archaea/eukaryota	Interproscan
IPR006638 all species →	Domain	Elp3/MiaA/NifB-like, radical SAM core domain	Interproscan
IPR005839 all species →	Family	Methylthiotransferase	Interproscan
IPR013848 all species →	Domain	Methylthiotransferase, N-terminal	Interproscan
IPR038135 all species →	Homologous_superfamily	Methylthiotransferase, N-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11918 all species →	RADICAL SAM PROTEINS	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0051539 all species →	Molecular Function	4 iron, 4 sulfur cluster binding	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0051536 all species →	Molecular Function	iron-sulfur cluster binding	Interproscan
GO:0035598 all species →	Molecular Function	N6-threonylcarbomyladenosine methylthiotransferase activity	Interproscan
GO:0035600 all species →	Biological Process	tRNA methylthiolation	Interproscan
GO:0006400 all species →	Biological Process	tRNA modification	Interproscan
GO:0016740 all species →	Molecular Function	transferase activity	Interproscan
GO:0035596 all species →	Molecular Function	methylthiotransferase activity	Interproscan
GO:0005783 all species →	Cellular Component	endoplasmic reticulum	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
K15865	CDKAL1; threonylcarbamoyladenosine tRNA methylthiotransferase CDKAL1	EC:2.8.4.5	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 →