Gene detail

Detailed information of asel_s0041.g97.t1 in Acropora selago

Genomic Location: sc0000041_pilon:1214413...1225197
NR annotation: XP_015761131.1, PREDICTED: eukaryotic translation initiation factor 3 subunit F-like [Acropora digitifera]
Species Acropora selago · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

asel_s0041.g97.t1

TCCGTTGAAAAGTCTTCGATTGAAATTCGAAGCTCTTTTGGCGTTCCACACAATGAATCTCAAGACGAGGTTGCTATTGAATTGGAGTATGCCAAAAGTATGTTTGAGCTACACAAGAAAGCTCATCCCAATGATGAAATAATTGGATGAAAAAGGAAACTGTTACAGCAAAAAAAACTGGTACCGAGCGAGGGTCCATGCGGGCAGAATTCAAGATGGCGACCACTGAAACTAGAAGAGCTCGGAAGGTTTATGTGCATCCTGTTGTATTGTTTTCAATCGTTGACGGCTTTGAAAGGCGTTCAGAAGATGCTAAAAGGGTTATAGGAACTCTCCTTGGATCCGTTGAAAAGTCTTCGATTGAAATTCGAAGCTCTTTTGGCGTTCCACACAATGAATCTCAAGACGAGGTTGCCATTGAATTGGAGTATGCCAAAAGTATGTTTGAGCTGCACAAGAAAGCTCATCCCAATGATGAAATAGTTGGATGGTATGCCACAGGATCTGACGTTACAGAACATTCCTTATTGATACACGAGTATTACTCAAGGGAAGCTAGCAACCCTGTTCATCTCACCATAGACACAACACTCAAAGGATCACAGATGGGAATCCGAGCTTATCAGAGCTGCAAAATGGGTGTCCCAGGAAAGACAGAGGGTACTATCTTCTCACCTGTGCCATGTGAAGTAATTTTGAACGGTCCGGAAAGAGTTGGAGTAAACTGGCTCCAGAGAACAAAAAGCACGTCTAGGCAAAGCCTCAAACCCTTGTCAGAAATGCAGCATGTGAGCAGTGCAAGTGAAACATTGTTGGAAATGCTTGAATCAGTAGTGTCGTACGTCGATGATGTTTTGGCTGGAAAAGTTCCCGGCGATAACAGTGTTGGCAGAGAGTTAATGGATCTGGTGACATCAGTTCCTCGCATGTCTAAAGAAGAATTTGAATCTATTCTCAACAGCAATATGCAGGACCTGCTGATGATTGTGTATTTATCAGGTCTTTGTAAGACGCAGATATCCCTCGGAGAAAAACTCGCCACCGTGTTATGATGTAACGTATTCGAAAGTCCAGTTAAATTTATCAAAAATATAAATCCATTGAGCTGTCGATCAGCTTTTCTTTGAAACCAAATCTTTCATGCAGGTGTTTATTACTGTGGCGTGTTTTCTTAGTCGAGAAGACTAACTTGGAATTATTTTCTAAACATTTTTATGCTGGTTTGACCTTGTTAATGCCTGCAGAATGGCAAGAGCGTGGGCCAGGGCGATCACGATCACGTACGAGACGCTTCTCCATTGGCTATTCGCGTCACGCGTACTTCCAATAGAAAGGAGGGTGGGCGTAAAGCATTTGAGAATGATGTTCTTAAAAGAGCGCAGAGCTCTTGCGTTTTTTCTCTATGACCTTATTAGCAAAAATTCCGGTTAACTCACGAGTAAGCGAATTCAAACTCAGTCGGCAAGAACAAGTGAAAAACGTTCAATAAGGTCTTCGGCGTATATTCCATGAAATGCCACCATCTTGGCTTGTACTGGCGAGGAGATTCGACGAAAAACTGGAGGGGGCCTGGGAGTGTGGTTGTTCCTCACTCCTGCTCTGTGAAGACTGAAAACGCTTCTGCAAAGATGATGGCGCCATCGGCTTAAATCGTGATGAATGATAAATCAGCAGAAACCGGCCTGTAACCGGATTAGTATTAGAGGGGAGTTAAGTGTTCTAAAACGCACCTTGACGGCTGATTTGTGGGGCAATTTTCGAGGAGCCGAAGTCAATGGAAACTTAAGACGCAAAGCGCGCAAATGAGTATGCATTGAATGGGATTCAAGACATTTGTCCATCCAGAAAAGCCACTTAATAGTGAAGCATCTATTTGAATGGTAACCCGGGGGCTTGCGATAACCTTCGTTGTGTCATGTTACGGAATCTGGGATATGCTCCAGCCCATGTGTGGCTTGGGGGGTTTGTTGTGGGAAAATGGAGAGGGAAGGAATGTTTTTTTTTAACAAATGGCCGCTTTTGAAGGCAAAAACTTCTAAGAGCTAGAAAAACCGGAAAGTTAATTATTTCGGTTTATCATATAATTACTATGAATCGAAAATGCGAACACTATATAATTatgaatgaattttttgatcattgcattttagcactgcttaggcagcagcgagaaagaccggaaaaattcaggccagaacgaaaattcgaaccctgacctctgcgatgccgttgcagttctcaaataaataaaaaaaattcat

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O00303	Eukaryotic translation initiation factor 3 subunit F OS=Homo sapiens OX=9606 GN=EIF3F PE=1 SV=1
Q4R5B8	Eukaryotic translation initiation factor 3 subunit F OS=Macaca fascicularis OX=9541 GN=EIF3F PE=2 SV=1
A5A6I3	Eukaryotic translation initiation factor 3 subunit F OS=Pan troglodytes OX=9598 GN=EIF3F PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005877 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01398 all species →	JAB	JAB1/Mov34/MPN/PAD-1 ubiquitin protease	Family	Interproscan
PF13012 all species →	MitMem_reg	Maintenance of mitochondrial structure and function	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027531 all species →	Family	Eukaryotic translation initiation factor 3 subunit F	Interproscan
IPR000555 all species →	Domain	JAB1/MPN/MOV34 metalloenzyme domain	Interproscan
IPR037518 all species →	Domain	MPN domain	Interproscan
IPR024969 all species →	Domain	EIF3F/CSN6-like, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10540 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003743 all species →	Molecular Function	translation initiation factor activity	Interproscan
GO:0005852 all species →	Cellular Component	eukaryotic translation initiation factor 3 complex	Interproscan
GO:0006413 all species →	Biological Process	translational initiation	Interproscan
GO:0031369 all species →	Molecular Function	translation initiation factor binding	Interproscan
GO:0071541 all species →	Cellular Component	eukaryotic translation initiation factor 3 complex, eIF3m	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0008233 all species →	Molecular Function	peptidase activity	Interproscan
GO:0008237 all species →	Molecular Function	metallopeptidase 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
K03249	EIF3F; translation initiation factor 3 subunit F	-	Exosome	ko04147	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of asel_s0041.g97.t1 across 24 RNA-seq samples of Acropora selago. 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.

24Samples

23TPM > 0

1Conditions

173.0Max TPM

121.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
coral larvae	24	23	121.48	173.03

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR14308027	coral larvae	coral larvae	not recorded	not recorded	SRP315987	173.03
SRR14308018	coral larvae	coral larvae	not recorded	not recorded	SRP315987	163.82
SRR14308012	coral larvae	coral larvae	not recorded	not recorded	SRP315987	151.11
SRR14308024	coral larvae	coral larvae	not recorded	not recorded	SRP315987	145.04
SRR14308007	coral larvae	coral larvae	not recorded	not recorded	SRP315987	135.85
SRR14308013	coral larvae	coral larvae	not recorded	not recorded	SRP315987	135.72
SRR14308010	coral larvae	coral larvae	not recorded	not recorded	SRP315987	134.82
SRR14308019	coral larvae	coral larvae	not recorded	not recorded	SRP315987	132.65
SRR14308017	coral larvae	coral larvae	not recorded	not recorded	SRP315987	131.03
SRR14308008	coral larvae	coral larvae	not recorded	not recorded	SRP315987	129.99
SRR14308011	coral larvae	coral larvae	not recorded	not recorded	SRP315987	129.08
SRR14308015	coral larvae	coral larvae	not recorded	not recorded	SRP315987	129.03
SRR14308025	coral larvae	coral larvae	not recorded	not recorded	SRP315987	126.43
SRR14308006	coral larvae	coral larvae	not recorded	not recorded	SRP315987	125.10
SRR14308016	coral larvae	coral larvae	not recorded	not recorded	SRP315987	117.04
SRR14308022	coral larvae	coral larvae	not recorded	not recorded	SRP315987	114.21
SRR14308023	coral larvae	coral larvae	not recorded	not recorded	SRP315987	112.04
SRR14308004	coral larvae	coral larvae	not recorded	not recorded	SRP315987	110.82
SRR14308020	coral larvae	coral larvae	not recorded	not recorded	SRP315987	109.46
SRR14308026	coral larvae	coral larvae	not recorded	not recorded	SRP315987	108.46
SRR14308009	coral larvae	coral larvae	not recorded	not recorded	SRP315987	106.88
SRR14308021	coral larvae	coral larvae	not recorded	not recorded	SRP315987	100.06
SRR14308014	coral larvae	coral larvae	not recorded	not recorded	SRP315987	93.93
SRR14308005	coral larvae	coral larvae	not recorded	not recorded	SRP315987	0.00

Source: CnidoSite RNA-seq expression matrices (ASELA_TPM, StringTie quantification over 24 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 Acropora selago 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	30	asel_s0050.g72.t1	0.89660094685689
Negatively correlated	17	asel_s0024.g70.t1	-0.865918334078928

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 Acropora selago, 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.

DNA methylation (bisulphite samples)

Sample	Methylation profile
Coral_Fragment_Parent	open
Larval_Pool_Offspring	open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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 →