Gene detail

Detailed information of KXJ23367.1 in Exaiptasia diaphana

Genomic Location: LJWW01000068.1:625072...638455
NR annotation: XP_020912888.1, uncharacterized protein LOC110250626 isoform X1 [Exaiptasia diaphana]
Species Exaiptasia diaphana · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A5DN78	Elongation factor Tu, mitochondrial OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) OX=294746 GN=TUF1 PE=3 SV=1
Q0BUQ2	Elongation factor Tu OS=Granulibacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1) OX=391165 GN=tuf PE=3 SV=1
Q2W2H3	Elongation factor Tu OS=Paramagnetospirillum magneticum (strain ATCC 700264 / AMB-1) OX=342108 GN=tuf1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003933 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03143 all species →	GTP_EFTU_D3	Elongation factor Tu C-terminal domain	Domain	Interproscan
PF00009 all species →	GTP_EFTU	Elongation factor Tu GTP binding domain	Domain	Interproscan
PF03144 all species →	GTP_EFTU_D2	Elongation factor Tu domain 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR033720 all species →	Domain	Elongation factor Tu, domain 2	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR000795 all species →	Domain	Translational (tr)-type GTP-binding domain	Interproscan
IPR050055 all species →	Family	Elongation factor Tu GTPase	Interproscan
IPR004160 all species →	Domain	Translation elongation factor EFTu/EF1A, C-terminal	Interproscan
IPR004541 all species →	Family	Translation elongation factor EFTu/EF1A, bacterial/organelle	Interproscan
IPR009001 all species →	Homologous_superfamily	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Interproscan
IPR041709 all species →	Domain	Elongation factor Tu (EF-Tu), GTP-binding domain	Interproscan
IPR009000 all species →	Homologous_superfamily	Translation protein, beta-barrel domain superfamily	Interproscan
IPR031157 all species →	Conserved_site	Tr-type G domain, conserved site	Interproscan
IPR004161 all species →	Domain	Translation elongation factor EFTu-like, domain 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43721 all species →	ELONGATION FACTOR TU-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0003746 all species →	Molecular Function	translation elongation factor activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006414 all species →	Biological Process	translational elongation	Interproscan
GO:0070125 all species →	Biological Process	mitochondrial translational elongation	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
K02358	tuf, TUFM; elongation factor Tu	-	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 KXJ23367.1 across 72 RNA-seq samples of Exaiptasia diaphana. 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.

72Samples

70TPM > 0

2Conditions

191.2Max TPM

104.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole animal · aposymbiotic	36	34	91.48	122.46
whole animal · symbiotic	36	36	116.46	191.21

Per sample · hover a bar for the full sample record

Show the sample table (72 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6202239	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	122.46
SRR6202240	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	121.87
SRR6202205	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	119.12
SRR6202210	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	116.99
SRR6202211	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	116.56
SRR6202237	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	111.86
SRR6202203	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	111.68
SRR6202212	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	111.47
SRR6202363	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	109.73
SRR6202235	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	108.49
SRR6202357	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	107.68
SRR6202207	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	106.34
SRR6202209	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	106.05
SRR6202256	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	105.44
SRR6202255	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	105.43
SRR6202208	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	105.40
SRR6202254	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	104.52
SRR6202204	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	103.93
SRR6202238	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	103.24
SRR6202257	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	99.00
SRR6202236	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	98.35
SRR6202206	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	89.42
SRR6202260	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	86.64
SRR6202358	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	84.63
SRR6202344	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	79.72
SRR6202241	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	76.71
SRR6202261	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	76.39
SRR6202242	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	75.78
SRR6202346	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	74.75
SRR6202258	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	74.53
SRR6202233	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	72.17
SRR6202259	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	69.57
SRR6202234	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	69.09
SRR6202343	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	68.26
SRR6202345	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	0.00
SRR6202364	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	0.00
SRR6202353	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	191.21
SRR6202349	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	180.09
SRR6202347	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	154.00
SRR6202354	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	151.31
SRR6202352	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	150.13
SRR6202351	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	148.25
SRR6202356	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	145.04
SRR6202337	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	143.96
SRR6202280	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	142.35
SRR6202281	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	140.20
SRR6202279	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	134.24
SRR6202338	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	132.22
SRR6202350	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	127.95
SRR6202276	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	127.25
SRR6202277	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	121.30
SRR6202278	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	116.50
SRR6202355	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	113.76
SRR6202348	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	113.28
SRR6202340	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	110.08
SRR6202341	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	110.08
SRR6202339	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	107.41
SRR6202263	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	106.30
SRR6202262	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	104.95
SRR6202309	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	97.85
SRR6202310	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	95.29
SRR6202283	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	92.18
SRR6202303	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	91.92
SRR6202282	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	91.59
SRR6202342	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	89.72
SRR6202308	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	86.42
SRR6202307	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	84.88
SRR6202306	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	83.73
SRR6202284	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	80.28
SRR6202304	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	78.68
SRR6202305	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	76.15
SRR6202285	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	72.03

Source: CnidoSite RNA-seq expression matrices (EDIAP_TPM, StringTie quantification over 72 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 Exaiptasia diaphana 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	25	KXJ19715.1	0.831323842272709
Negatively correlated	62	KXJ26459.1	-0.826898290429443

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 Exaiptasia diaphana, 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.

Peak calls overlapping this gene

Assay	Sample	Peaks	Region
ATAC-seq	Stress_Day21_Sym	2	Promoter (2-3kb) 1 · Intron 1

Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.

DNA methylation (bisulphite samples)

Sample	Methylation profile
whole_animal_aposymbiotic_1	open
whole_animal_aposymbiotic_2	open
whole_animal_aposymbiotic_3	open
whole_animal_aposymbiotic_4	open
whole_animal_aposymbiotic_5	open
whole_animal_aposymbiotic_6	open
whole_animal_aposymbiotic_7	open
whole_animal_aposymbiotic_8	open
whole_animal_aposymbiotic_9	open
whole_animal_symbiotic_1	open
whole_animal_symbiotic_10	open
whole_animal_symbiotic_11	open
whole_animal_symbiotic_12	open
whole_animal_symbiotic_13	open
whole_animal_symbiotic_14	open
whole_animal_symbiotic_2	open
whole_animal_symbiotic_3	open
whole_animal_symbiotic_4	open
whole_animal_symbiotic_5	open
whole_animal_symbiotic_6	open
whole_animal_symbiotic_7	open
whole_animal_symbiotic_8	open
whole_animal_symbiotic_9	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 →