Gene detail

Detailed information of KXJ12640.1 in Exaiptasia diaphana

Genomic Location: LJWW01000314.1:86266...93193
NR annotation: XP_020903380.1, signal recognition particle 54 kDa protein [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
Q7ZVN5	Signal recognition particle subunit SRP54 OS=Danio rerio OX=7955 GN=srp54 PE=2 SV=1
P14576	Signal recognition particle subunit SRP54 OS=Mus musculus OX=10090 GN=Srp54 PE=1 SV=2
Q2T9U1	Signal recognition particle subunit SRP54 OS=Bos taurus OX=9913 GN=SRP54 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003673 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00448 all species →	SRP54	SRP54-type protein, GTPase domain	Domain	Interproscan
PF02978 all species →	SRP_SPB	Signal peptide binding domain	Domain	Interproscan
PF02881 all species →	SRP54_N	SRP54-type protein, helical bundle domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036891 all species →	Homologous_superfamily	Signal recognition particle, SRP54 subunit, M-domain superfamily	Interproscan
IPR013822 all species →	Domain	Signal recognition particle SRP54, helical bundle	Interproscan
IPR000897 all species →	Domain	Signal recognition particle, SRP54 subunit, GTPase domain	Interproscan
IPR004125 all species →	Domain	Signal recognition particle, SRP54 subunit, M-domain	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR006325 all species →	Family	Signal recognition particle, SRP54 subunit, eukaryotic	Interproscan
IPR022941 all species →	Family	Signal recognition particle, SRP54 subunit	Interproscan
IPR042101 all species →	Homologous_superfamily	Signal recognition particle SRP54, N-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11564 all species →	SIGNAL RECOGNITION PARTICLE 54K PROTEIN SRP54	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006614 all species →	Biological Process	SRP-dependent cotranslational protein targeting to membrane	Interproscan
GO:0008312 all species →	Molecular Function	7S RNA binding	Interproscan
GO:0048500 all species →	Cellular Component	signal recognition particle	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005786 all species →	Cellular Component	signal recognition particle, endoplasmic reticulum targeting	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006616 all species →	Biological Process	SRP-dependent cotranslational protein targeting to membrane, translocation	Interproscan
GO:0030942 all species →	Molecular Function	endoplasmic reticulum signal peptide binding	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
K03106	SRP54, ffh; signal recognition particle subunit SRP54	EC:3.6.5.4	Secretion system	ko02044	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of KXJ12640.1 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

305.5Max TPM

82.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole animal · aposymbiotic	36	35	79.44	305.46
whole animal · symbiotic	36	35	85.34	134.28

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
SRR6202345	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	305.46
SRR6202343	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	98.23
SRR6202357	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	91.84
SRR6202344	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	90.40
SRR6202258	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	86.51
SRR6202240	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	81.82
SRR6202212	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	81.37
SRR6202260	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	81.16
SRR6202242	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	81.02
SRR6202257	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	80.90
SRR6202209	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	79.49
SRR6202211	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	78.60
SRR6202234	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	78.14
SRR6202241	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	76.30
SRR6202233	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	75.36
SRR6202346	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	75.34
SRR6202203	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	75.03
SRR6202207	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	73.68
SRR6202259	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	73.57
SRR6202210	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	73.55
SRR6202261	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	72.88
SRR6202206	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	72.15
SRR6202239	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	71.93
SRR6202238	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	71.70
SRR6202208	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	70.82
SRR6202205	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	70.64
SRR6202256	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	68.35
SRR6202255	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	68.01
SRR6202358	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	67.79
SRR6202254	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	67.45
SRR6202204	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	66.55
SRR6202237	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	66.51
SRR6202235	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	63.60
SRR6202236	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	62.12
SRR6202363	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	61.68
SRR6202364	whole animal · aposymbiotic	whole animal	not recorded	aposymbiotic	SRP120942	0.00
SRR6202349	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	134.28
SRR6202352	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	107.18
SRR6202280	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	103.59
SRR6202347	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	103.52
SRR6202356	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	101.97
SRR6202307	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	97.98
SRR6202309	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	97.33
SRR6202310	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	95.65
SRR6202342	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	94.86
SRR6202282	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	94.34
SRR6202281	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	94.10
SRR6202351	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	92.74
SRR6202279	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	90.54
SRR6202350	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	88.75
SRR6202277	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	86.98
SRR6202337	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	85.78
SRR6202308	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	85.20
SRR6202283	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	84.68
SRR6202338	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	84.67
SRR6202278	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	84.03
SRR6202284	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	83.16
SRR6202355	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	82.78
SRR6202348	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	81.84
SRR6202276	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	80.65
SRR6202339	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	80.31
SRR6202306	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	79.37
SRR6202354	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	78.73
SRR6202304	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	78.27
SRR6202263	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	76.76
SRR6202305	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	76.55
SRR6202340	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	75.73
SRR6202285	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	74.64
SRR6202262	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	73.81
SRR6202341	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	72.86
SRR6202303	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	68.67
SRR6202353	whole animal · symbiotic	whole animal	not recorded	symbiotic	SRP120942	0.00

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	13	KXJ19221.1	0.863394153456864
Negatively correlated	16	KXJ18667.1	-0.695795765247711

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

No called peak overlaps this gene in 2 available assays. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

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 →