Gene detail

Detailed information of FUN_014584-T1 in Dendrogyra cylindrus

Genomic Location: contig_22:6064637...6076261
NR annotation: XP_020626143.1, diphthine--ammonia ligase-like [Orbicella faveolata]
Species Dendrogyra cylindrus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

FUN_014584-T1

ATGAGGGTTGTTGCATTAATCAGCGGAGGAAAGGATAGTTGTTACAACATGGTGCAATGTGTACAACAAGGCCATACTATTGTGGCACTGGCAAATCTGAAGCCAAGAGATGGAGCTGATGAACTTGATAGTTACATGTACCAGACGGTTGGTCACAATGCCATTGATCTGTATGCACAAGCTATGGACTTGCCGTTGTATCGGGGGACAATTCAGGGTTCCTCTGTGGATCAAGGCAAAGTGTATACAGAAAATCAGCAAGATGAGGTTGAAGACCTGTACAAGCTGCTAAACAATATCAAGGAGGATATTGCATTTGATGCAGTGTCAGCTGGAGCAATTTTATCAGACTACCAAAGAGTTAGAGTGGAAAATGTGTGTTCCCGATTGGGATTATCTTCACTGGCTTACTTGTGGAGACGTGACCAAACCGAACTACTTAGTGAAATGATCTCCTCAGGAATTGAAGCTGTGTTAATCAAAGTGGCTGTAATGGATTTAAGCCCAAAAAGACACCTGGGGCTGCCAATATCAGAAGTTTATTCTCTAATGTGCAAACTGAACCACAAGTATGGCTCAAATGTTTGTGGAGAAGGTGGCGAGTATGAAACATTTACTTTGGATTGCCCATTGTTCAAGCGAAAAATAGTCATAGATGAAAGTGATGTTGTCATTCATTCTGATGATGCATTTGCTCCTGTGGGGTTCCTTCGCTTTAAGAAAATGCATGTGCAGGAGAAGGAAGTAACCAAGGGCAGCTCTGGTCTGTATCTTAAAGATCACACATGTACAGAATCGTTAGACAAGTTGCAGATACAGCCAGATAATATAACAAATACTGAACAAGGCAGCAACATCAGGAATAAAGAACAACAAATAAAGATCCCTGTGAGGaaacaagaacaaaagaaaGATCATGTCCTCTACAGCAGGTGTGGAAATTATATTTGGGTTTCTGGAATTTATGGCCATTCCACCTTTGATGAAAGAACACTGTCAGTTGAAGACATAACAAGAAGTGTTTTACAAAACTTGCAAGATACACTCACTAATTTGGAGGCAAACTTGTGTAATGGAATGATAGTTCACCTTTTTGTGAAAAACATGGATGATTTTGCAAAAATCAACTCAGtttataaaacatttttaagaGTGAACCCTCCTGCaagAGCATGTATCCAGCTGAACTTGCCGGAAGACATTGCCATCCAGGTTGATTGTCTTGTTTATGCTGCCCAAAGTGCTGATGCTTCAACACGGGAAGCTATGCATGTTCAAAGCATTTCTCACTGGGCACCAGCAAATATTGGTCCTTACAGCCAGGCAACTAAGGCTGGGGACACCTTATTTGTCTCTGGTTCAATTGGTTTGTGGCCACCAACAATGACAATGATCCAAGGTGGCATTACAAAAGAAGCTTCCCTATCATTGCAACATGTTGACAGAGTCATATCAGCTCTTAATCCAGCAGAATCACTACAAAGTGTTGTTCATGGATTTTGTTTTCTAACTTCAACTGCTTATGTGGCAGTTGCAAAGGATACTTGGTATCAAGCGTCAAATGCGAAGAGCAAAGACAGCATGGAGCAAGACCGAGCACCTGTAGGGTTAATGTCATATGTCATTGTGCCTGCATTACCAAAGGGAGCTCTGGTTGAATGGCATGTTGTGGCACTGGAAAATCAGATCCAGCATCAGTATGACTCAACTTCAGTGTGCAGGGGGAGCTTCAGTGTCAATGTACAGAGCATTGCTGTTACAGGAAATCATAACAACAGCATTGCTGTTAACATTGTTGTTGAGTGTACATCTAATGAGTGCAACTTGGAGGAAATAATGGACACATTTGTCAGTGAGTTAAAATGCTGCACTTCACAGCACAACATTGGCCTCTCTCATCTGATGTATATGAGGATATTTTATGTCAAAGACATTATGGACCATTGGCATGCACAGGACTTTATTCATAGGAGTTTGGAGAGAACTGTTGTTCCTGCACCTGCATTTTCTCTGATACCTGTGGATGGTCTCGAAACAGAGAGAGCTGTTCTGCTTTTCTGTTGCCTTCTACAGAAACCTGGAGATGGTACACTAGACTACTGA

Transcript

FUN_014584-T1

TCAAAGTGGCGGCCAGATGGGAGATGGTGGTATGAACGTAATGAAAAATACGGCCAGTTTGTAGCTACAACAGCTTAGTAACGAGTTGTTTTCCTTGCAGCCATGAGGGTTGTTGCATTAATCAGCGGAGGAAAGGATAGTTGTTACAACATGGTGCAATGTGTACAACAAGGCCATACTATTGTGGCACTGGCAAATCTGAAGCCAAGAGATGGAGCTGATGAACTTGATAGTTACATGTACCAGACGGTTGGTCACAATGCCATTGATCTGTATGCACAAGCTATGGACTTGCCGTTGTATCGGGGGACAATTCAGGGTTCCTCTGTGGATCAAGGCAAAGTGTATACAGAAAATCAGCAAGATGAGGTTGAAGACCTGTACAAGCTGCTAAACAATATCAAGGAGGATATTGCATTTGATGCAGTGTCAGCTGGAGCAATTTTATCAGACTACCAAAGAGTTAGAGTGGAAAATGTGTGTTCCCGATTGGGATTATCTTCACTGGCTTACTTGTGGAGACGTGACCAAACCGAACTACTTAGTGAAATGATCTCCTCAGGAATTGAAGCTGTGTTAATCAAAGTGGCTGTAATGGATTTAAGCCCAAAAAGACACCTGGGGCTGCCAATATCAGAAGTTTATTCTCTAATGTGCAAACTGAACCACAAGTATGGCTCAAATGTTTGTGGAGAAGGTGGCGAGTATGAAACATTTACTTTGGATTGCCCATTGTTCAAGCGAAAAATAGTCATAGATGAAAGTGATGTTGTCATTCATTCTGATGATGCATTTGCTCCTGTGGGGTTCCTTCGCTTTAAGAAAATGCATGTGCAGGAGAAGGAAGTAACCAAGGGCAGCTCTGGTCTGTATCTTAAAGATCACACATGTACAGAATCGTTAGACAAGTTGCAGATACAGCCAGATAATATAACAAATACTGAACAAGGCAGCAACATCAGGAATAAAGAACAACAAATAAAGATCCCTGTGAGGaaacaagaacaaaagaaaGATCATGTCCTCTACAGCAGGTGTGGAAATTATATTTGGGTTTCTGGAATTTATGGCCATTCCACCTTTGATGAAAGAACACTGTCAGTTGAAGACATAACAAGAAGTGTTTTACAAAACTTGCAAGATACACTCACTAATTTGGAGGCAAACTTGTGTAATGGAATGATAGTTCACCTTTTTGTGAAAAACATGGATGATTTTGCAAAAATCAACTCAGtttataaaacatttttaagaGTGAACCCTCCTGCaagAGCATGTATCCAGCTGAACTTGCCGGAAGACATTGCCATCCAGGTTGATTGTCTTGTTTATGCTGCCCAAAGTGCTGATGCTTCAACACGGGAAGCTATGCATGTTCAAAGCATTTCTCACTGGGCACCAGCAAATATTGGTCCTTACAGCCAGGCAACTAAGGCTGGGGACACCTTATTTGTCTCTGGTTCAATTGGTTTGTGGCCACCAACAATGACAATGATCCAAGGTGGCATTACAAAAGAAGCTTCCCTATCATTGCAACATGTTGACAGAGTCATATCAGCTCTTAATCCAGCAGAATCACTACAAAGTGTTGTTCATGGATTTTGTTTTCTAACTTCAACTGCTTATGTGGCAGTTGCAAAGGATACTTGGTATCAAGCGTCAAATGCGAAGAGCAAAGACAGCATGGAGCAAGACCGAGCACCTGTAGGGTTAATGTCATATGTCATTGTGCCTGCATTACCAAAGGGAGCTCTGGTTGAATGGCATGTTGTGGCACTGGAAAATCAGATCCAGCATCAGTATGACTCAACTTCAGTGTGCAGGGGGAGCTTCAGTGTCAATGTACAGAGCATTGCTGTTACAGGAAATCATAACAACAGCATTGCTGTTAACATTGTTGTTGAGTGTACATCTAATGAGTGCAACTTGGAGGAAATAATGGACACATTTGTCAGTGAGTTAAAATGCTGCACTTCACAGCACAACATTGGCCTCTCTCATCTGATGTATATGAGGATATTTTATGTCAAAGACATTATGGACCATTGGCATGCACAGGACTTTATTCATAGGAGTTTGGAGAGAACTGTTGTTCCTGCACCTGCATTTTCTCTGATACCTGTGGATGGTCTCGAAACAGAGAGAGCTGTTCTGCTTTTCTGTTGCCTTCTACAGAAACCTGGAGATGGTACACTAGACTACTGATATCAATTAACTTGCCTGAAAAAATGTCTTTTATGTTCTCAACAGATGAAGATAacttatatacatgtatgtagatGTCCTGCCAGAGGGCGAGGGAGGGTTTCCCATGTCCCAAAATATCCAGAGTCATTGCATTGTTGGTAAGAAATTGAGCGAGTGTTGCAAATAATTTAAAGAAGTCCCTTGTTGGTGTTTCATCATACTTTACGTCGCTTGACATTGCCAACACTTTTGGAATTTTGGCGAAAAGGGGCGTCTTTTGTCACGATTTCACTACTTTTTGGGTCATGTTGAATGTGTAACACGCACTGTTCAGT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A2RV01	Diphthine--ammonia ligase OS=Danio rerio OX=7955 GN=dph6 PE=2 SV=1
Q2HJF5	Diphthine--ammonia ligase OS=Bos taurus OX=9913 GN=DPH6 PE=2 SV=1
Q9USQ7	Diphthine--ammonia ligase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=mug71 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003404 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01902 all species →	Diphthami_syn_2	Diphthamide synthase	Family	Interproscan
PF01042 all species →	Ribonuc_L-PSP	Endoribonuclease L-PSP	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035959 all species →	Homologous_superfamily	RutC-like superfamily	Interproscan
IPR002761 all species →	Domain	Diphthamide synthase domain	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR006175 all species →	Family	YjgF/YER057c/UK114 family	Interproscan
IPR030662 all species →	Family	Diphthine--ammonia ligase/Uncharacterised protein MJ0570	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12196 all species →	DOMAIN OF UNKNOWN FUNCTION 71 DUF71 -CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0017178 all species →	Molecular Function	diphthine-ammonia ligase activity	Interproscan
GO:0017183 all species →	Biological Process	protein histidyl modification to diphthamide	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
K06927	DPH6; diphthine-ammonia ligase	EC:6.3.1.14	Translation factors	ko03012	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 →