Gene detail

Detailed information of eanc_s042.g0200.t1 in Fimbriaphyllia ancora

Genomic Location: s042:3050568...3068362
NR annotation: XP_020609660.1, regulator of nonsense transcripts 1-like [Orbicella faveolata]
Species Fimbriaphyllia ancora · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

eanc_s042.g0200.t1

CACGTTCTTGTGCTAAAATTTGAAATTGTTCGGGTTTTTCGGTTTGGTTGGCGAAAGCATCGACTTTTTAACGTTTCTTCGCTTTGAAGATGAGCACTGTAGACTCTTATGGGCCTGCATCTCAAACACTCACTTTTTTAGACACCGAAGAAGCTGATTTCGGAGCAGATACTCAAGGAAGCGAGTACGAATTTCACGATTTTACTGTCCCATCGCAAACTCAAACTCAGTCGCAAGCTTCGCAGCCTGAAGGCAGCCAACCTTTGGTCAATGGAAATGCCGTGGATCAAAAAGAGGAGCTTAGTAACGGTCCAGTGCCAGGAAATGAAGATACGACAGTAGACAGTGGGGTTTCCAAGGTTAGCAACTCTTTGGGAGAGCTAAACTTCGAGGAGGACGAAGACGAAACCTTTTACACAAAAGATCTGCCAGCCTACGCTTGCAGATATTGTGGAGTTCATGACCCAGCATCTGTTGTTCAGTGCATTCAGTGTAAGAAATGGTTTTGTAATGGTCGAGGGAATACTGCCGGCAGCCACATTGTCAACCACCTGGTTAGAGCCAAACACAAAGAGGTTACTCTTCACAAGGATGGACCCCTTGGGGAAACAATTCTGGAGTGCTACAACTGCGCCTGTCGCAATGTGTTCTTGTTGGGCTTTATCCCAGCCAAGGCTGACTCTGTTGTGGTGTTGCTTTGTAGGCAGCCATGTGCAACACAGAGTAACTCAAAGGACATGAACTGGGACCAAGCACAATGGCAACCTTTGATAAATGACCGCTGCTTTTTGTCCTGGCTTGTCAAAGTTCCATCTGACGAGGATCAGCTAAGGGCAAGACAGATTTCAGCCCAGCAAATTAACAAACTGGAAGAACTATGGAAGGATAACCCAGAAGCAAAGCTAGAGGATTTGGACAAACCTGGAGTTGATGATGAACCACAGCAAGTTCTGCTGAGGTATGAAGATGCTTACCAGTATCAGAACATCTTTGGGCCACTGGTTAAACTGGAGGCAGATTATGACAAGAAACTTAAGGAGTCACAGACTCAAGATAACATCGTTGTTCGTTGGGACATTGGTCTCAATAAGAAGAGGATTGCGTATTTCTCATTTCCTAAAACAAATGACGACATGCGGCTGATGCCTGGTGACGAACTGCGCCTGAGATATGTTGGTGAACTGCACAAACCCTGGCAGGGAGTTGGTCATGTTATCAAAGTACCAAACAACTTTGGTGAAGAAGTTGGAATTGAGTTACGTAGTAATCTGGGTGCTCCAGTTGAATGCACCCATAACTTTGTGGTGGACTTTGTGTGGAAATCAACCTCTTTTGACAGGATGCAGACTGGAATGAAGACCTTTGCAGTCGATGAGACGTCTGTCAGTGGGTACATTTATCACAAGCTTCTGGGACATGAGGTGGAGGAACAGGTTGTCAAGTGCCAGCTTCCTAAAAGGTTTTCGGCTCAAGGTTTACCCGAACTTAATCATTCCCAAGTTTATGCTGTGAAGACCGTACTCCAAAGACCACTTAGCCTTATTCAGGGCCCACCTGGTACTGGAAAGACTGTGACTTCTGCTAGTGTAGTCTATCACTTGGCTAAACAGAATAATGGACAAGTTCTTGTCTGTGCTCCCAGCAACATTGCTGTCGATCAACTCACGGAGAAGATCCACAAGACTGGACTTAAGGTTGTAAGACTGTGTGCCAAGAGTAGAGAGGCTATTGACTCTCCTGTAGCATTCCTAGCTCTGCACAATCAAGTACGTAATATGGACAGTGTCCCTGAACTTCAAAAACTTCAACAACTGAAAGATGAGCAAGGTGAGCTGTCTGCTGCTGACGAGAAAAGGTACCGGTCTCTCAAGAGGAACTGTGAACGAGAGCTGTTGCAGCATGCTGATGTGATATGCACCACATGTGTGGGTGCTGGTGATCCACGTCTGTCCAAGTTTAGGTTCCGTACTGTGTTGATTGACGAGTCTACACAGGCCACAGAGCCAGAGTGTATGGTGCCAGTTGTTCTTGGCTGCAAGCAGCTGATCCTGGTTGGAGATCATTGCCAGTTGGGTCCTGTTGTCATGTGCAAGAAAGCAGCCAATGCTGGTCTCTCTCAGTCTCTGTTTGAACGGTTGGTGGTTTTGGGAATCCGTCCTATACGCCTGCAAGTCCAGTACCGTATGCATCCTTCCTTGAGTGAGTTCCCATCCAATCTATTTTATGATGGAACACTTCAGAATGGAGTTACTGTTGCTGAGCGGCAACAGTCAGGTATTGACTTTCCATGGCCTGTTCCTGACAAACCAATGTTCTTCTATGCTACCATGGGTCAAGAGGAAATTGCCTCCTCTGGCACATCTTACCTTAACAGGACTGAAGCTGCAAATGTGGAGAAGATTGCCACACGTTTCCTACGTGCTGGCGTCAAGCCAGCACAGATTGGTGTGATTACTCCATACGAGGGTCAGAGGGCCTACATTGTACAGTACATGCAGTTCAGCGGCTCCCTGCATGCCAACCTTTACCTGGAAATCGAAGTGGCCAGTGTAGATGCTTTCCAGGGACGAGAGAAGGACTACATCATCCTGTCATGTGTGCGATCAAATGAACACCAGGGCATTGGCTTCTTGAATGATCCAAGACGTCTGAACGTAGCTTTGACTCGAGCAAAGTATGGCATCATTGTCATTGGCAATCCCAAAATTTTGTCCAGGCAACCGCTCTGGAACCATCTGTTGAATTACTATAAGGAGAACAAGGCTTTGATGGAAGGGCCACTGAACAATCTGAAGGAAAGCATGATCCAGTTTAGTAAACCAAGAAAGCTTGTCAACCGCACCAACCCGGGAGGCCGTTTCATGAGCACCACCATGTTTGACGCCCGTGAAGCGCTTGTCCGTGGCAGTGTGTATGATCGACAGATGCCTCCTGCGCCCATGGATCATCCCGCTGCTTTCCATGACACTTACTTCCACACTCACGATCGTCTGAGCTTCATCGGCGCTGAGCGCACCATTCCACCCGCTGCTGCTGCCAGGATCCCGGTACCTGTGGGAATGTTCATCCCCCCTGTACCACCCCCACATCACAACTACTTTGGACAGCCTCTGACGGGACGCATGCCACATGGTCGAGCAGTGCAGCAGCCCCGGCAGCGCAATCAACGGAACCATCACCCACACCAGCCAATGGCTTACGCTCCTCACATGCCAGCCAGCCAGGCAAGCCAGGATGCTTCTCAGCCTCTGTCCCAGGGTCCTTTGACTCAAGGCGGAATGTCCATGAGTCAGCCCATGGCTTCGCAGCCACTGTCCCAACCGGACTTGTCTCAAGACAGTTACCTGGGAGATGACTTGAACCTTAAGTCCCAGGCAGACGCGGTGCTGTCCCAGGACTCCACCTACCAAGGGGAGAGGGGAGGTTACATGAACTCCTTACCAGACTACTCCCAGCCAAACTATGCCTCCCAGTACTGAGTTGTCAGCCTCCCGGCTGATAAGGGGGCACGTTACCACCCGGAAGCCGTCGCTAAGGTAACTGGCATGGTTACGCCTTGCGAAAGCCACACCCTTGCTTTGCCCCGCACGGAAGGGTGTGGTCCCACCTTAACCTTGAAGTGGAACGAGAGCATGAAGAAGAAGACAGGAGAGAAGAttttttttttttttttttGCCGATTTTACAACGGCAACTCTTAACGGTTTTGACGCCGGAAACGACAACGAATGAACTGAGGAGCACAATTCTACTTTTATTGCGGACAATGGACGAGACAGTAAAACGAAGCAGCGATATCTGAAAATGACCGTGACCTTTGGTGGCGAGGCAATTTCCCGTCTCGAAAAAATTGGCGTCGACTCTTTTTCCCAAACGCTGAACCCTACTTAGCTCCCACAAGTCCACAACTTCTGTAGGTTACTTAGAAACACAAAGCAGTATCTGTCAGTAATAACGCCGCGAAAATCAGTGAAGTTGAGAAGAGCACGAGAGAAACGAGAGCAGTATTATTTTATCTTCCAACCTTATGCGAGGCTTACACTTTTAATACGTTAATTCAGTTGCAGAGGGATATTTCAGCTATTTTAAGCTGTCGCAATTCATATGATCATTCCTTCGGTAAAAAGTCACAGAACACTCGTAAGGGAAAAGAAACTCTCAAAGGTTCGGTATCACAGCTTCAACGCGTACTTAGTCGGTTCTTTGGAGCTGTTGTGCGTTAAGTACATTTTAAGAGTATCGTATCGTATTTTAAACCAACTCCGAAGGAAAATCGACGTTTACATTTTGAACTGAGTTTGTGCTTTTCTTTGAGTAAACATTGGCTGAAGGGTATATGTTTTACCAGGAAGTGTTGTTTTATGCGCTCTTTGTCTAACTGAACTGCCTGCTTGATTAAGAAGCGAAAAACTATAAAATCGCCACCTTATGCTTTCAGATAAGTAGATATAAGAATAAATGAAACAAGGCATGAACTAGATTTAAAATCAGTGTAAGAGTGGCCGCGGTTACCGTAGATCCCTTTGCCTTAGCGATTAGCCGCTCTCCGTCCTACGAAATAATTGCTCGGTTAGTGTTCAGGTTTCATCCGCTGCTTCAAGTACTGCTTCTACTGCTGCTAACAAGTGCCCAGGACAAAGTCAACTGGTTGCGTTTTACCTTGATTTGTCTGTTGGAGTCTAATAGACTGGGCTGTGTAGATGGTGTAAACGCGTCCCGTGAAAGTCGTTAAAAATCGGCCTTTTGTTACACCCTTTTCATGGTTATCTGTGATTCGGAATTTCACTTTAGCTTTTTAATATTTTAGTTAAGCAATTTGTTATGCTAAGTGTGTTCTTATTGCCCCATTTCTTGTGCTGGGGCAGGTAGTTGATTTCCCGCCGTACATTGTAACGACTCGACATAATTTTATCATCAAGGGCTGTAGTGTGCCCACTGGTTTACAATACACGTAATGACAACGAACCTGAGAGTACTTTTATTGTGTCTTAAATGGGTGATGTCAAAAGATGGACCGCCTAACTCGGGGTCGAAACGAGCTTGTCTCTGTTATATTTGAGCACCTAATGTTGTGAACCACTCCAAGTTGCGAGGAGTAAGCGCAAACTCTCTATTAAGCCCCACCCTCTCCCTCTGTTAACACTCCTATTTGAACCTCTCATCCAAATAATTGTTTTCTTGATCTCATCTTTTCCCCTAGTTTTCTGTCATGTGATGTAAGGCTTTGAAATTACATCCCTATTGTTAAATGATATGAAATCCACGGTTTTATCATTAGACTTCGTCAACAGATCGAACGAATCGATGCAGATTAGCTTCCACAAGCCAACCACAATGCAAAAGATTTCCTGACGAGGCTTTAGCTTGCGTTGGCAGATGGCTTTCTGACCAGTGTAAAAACAAGTGTAGCGATATTTAGAGTGGAATTGAGGAATAGAGAACTGTGAAGTAA

Transcript

eanc_s042.g0200.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9EPU0	Regulator of nonsense transcripts 1 OS=Mus musculus OX=10090 GN=Upf1 PE=1 SV=2
Q92900	Regulator of nonsense transcripts 1 OS=Homo sapiens OX=9606 GN=UPF1 PE=1 SV=2
F1RCY6	Regulator of nonsense transcripts 1 OS=Danio rerio OX=7955 GN=upf1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004432 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04851 all species →	ResIII	Type III restriction enzyme, res subunit	Family	Interproscan
PF09416 all species →	UPF1_Zn_bind	RNA helicase (UPF2 interacting domain)	Domain	Interproscan
PF13087 all species →	AAA_12	AAA domain	Domain	Interproscan
PF18141 all species →	UPF1_1B_dom	RNA helicase UPF1, 1B domain	Domain	Interproscan
PF13086 all species →	AAA_11	AAA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018999 all species →	Domain	RNA helicase UPF1, Cys/His rich zinc-binding domain	Interproscan
IPR047187 all species →	Domain	Upf1-like, C-terminal helicase domain	Interproscan
IPR006935 all species →	Domain	Helicase/UvrB, N-terminal	Interproscan
IPR040812 all species →	Domain	RNA helicase UPF1, 1B domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR041679 all species →	Domain	DNA2/NAM7 helicase-like, C-terminal	Interproscan
IPR041677 all species →	Domain	DNA2/NAM7 helicase, helicase domain	Interproscan
IPR045055 all species →	Family	DNA2/NAM7-like helicase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10887 all species →	DNA2/NAM7 HELICASE FAMILY	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase activity	Interproscan
GO:0004386 all species →	Molecular Function	helicase activity	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
K14326	UPF1, RENT1; regulator of nonsense transcripts 1	EC:5.6.2.5 EC:5.6.2.3	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of eanc_s042.g0200.t1 across 18 RNA-seq samples of Fimbriaphyllia ancora. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

18Samples

16TPM > 0

4Conditions

366.4Max TPM

87.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
ovaries	11	9	48.26	112.39
testes	5	5	80.79	102.55
Tentacles	1	1	366.41	366.41
Mouth and pharynx	1	1	268.87	268.87

Per sample · hover a bar for the full sample record

Show the sample table (18 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
DRR235375	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 126-200 um in diameter	not recorded	DRP006537	112.39
DRR235372	ovaries	ovaries	oocytes with cytoplasmic polarization\, <125 um in diameter	not recorded	DRP006537	99.65
DRR235377	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 126-200 um in diameter	not recorded	DRP006537	60.66
DRR235381	ovaries	ovaries	oocytes with 'U'-like germinal vesicles\, >276 um in diameter and GVBD	not recorded	DRP006537	45.23
DRR235376	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 126-200 um in diameter	not recorded	DRP006537	44.63
DRR235383	ovaries	ovaries	oocytes with 'U'-like germinal vesicles\, >276 um in diameter and GVBD	not recorded	DRP006537	44.21
DRR235378	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 201-275 um in diameter	not recorded	DRP006537	44.14
DRR235380	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 201-275 um in diameter	not recorded	DRP006537	41.11
DRR235382	ovaries	ovaries	oocytes with 'U'-like germinal vesicles\, >276 um in diameter and GVBD	not recorded	DRP006537	38.83
DRR235374	ovaries	ovaries	oocytes with cytoplasmic polarization\, <125 um in diameter	not recorded	DRP006537	0.00
DRR235379	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 201-275 um in diameter	not recorded	DRP006537	0.00
DRR235386	testes	testes	spermatogonia	not recorded	DRP006537	102.55
DRR235389	testes	testes	spermatogonia and primary spermatocytes	not recorded	DRP006537	99.65
DRR235387	testes	testes	spermatogonia and primary spermatocytes	not recorded	DRP006537	78.65
DRR235385	testes	testes	spermatogonia	not recorded	DRP006537	64.45
DRR235384	testes	testes	spermatogonia	not recorded	DRP006537	58.64
DRR397929	Tentacles	Tentacles	not recorded	not recorded	DRP011835	366.41
DRR397944	Mouth and pharynx	Mouth and pharynx	not recorded	not recorded	DRP011835	268.87

Source: CnidoSite RNA-seq expression matrices (FANCO_TPM, StringTie quantification over 18 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Fimbriaphyllia ancora 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	17	eanc_s050.g0198.t1	0.963544156723551
Negatively correlated	13	eanc_s008.g0511.t1	-0.842659789570991

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Fimbriaphyllia ancora, 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.	ready	open →
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 →