Gene detail

Detailed information of OS493_010276-T1 in Lophelia pertusa

Genomic Location: scaffold_25:618977...628210
NR annotation: KAJ7392625.1, H/ACA ribonucleoprotein complex subunit dkc1 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
F1Q749	H/ACA ribonucleoprotein complex subunit DKC1 OS=Danio rerio OX=7955 GN=dkc1 PE=2 SV=1
Q9ESX5	H/ACA ribonucleoprotein complex subunit DKC1 OS=Mus musculus OX=10090 GN=Dkc1 PE=1 SV=4
O60832	H/ACA ribonucleoprotein complex subunit DKC1 OS=Homo sapiens OX=9606 GN=DKC1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004107 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08068 all species →	DKCLD	DKCLD (NUC011) domain	Domain	Interproscan
PF16198 all species →	TruB_C_2	tRNA pseudouridylate synthase B C-terminal domain	Family	Interproscan
PF01509 all species →	TruB_N	TruB family pseudouridylate synthase (N terminal domain)	Family	Interproscan
PF01472 all species →	PUA	PUA domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012960 all species →	Domain	Dyskerin-like	Interproscan
IPR004521 all species →	Domain	Uncharacterised domain CHP00451	Interproscan
IPR015947 all species →	Homologous_superfamily	PUA-like superfamily	Interproscan
IPR032819 all species →	Domain	tRNA pseudouridylate synthase B, C-terminal	Interproscan
IPR004802 all species →	Family	tRNA pseudouridine synthase B family	Interproscan
IPR002501 all species →	Domain	Pseudouridine synthase II, N-terminal	Interproscan
IPR036974 all species →	Homologous_superfamily	PUA domain superfamily	Interproscan
IPR002478 all species →	Domain	PUA domain	Interproscan
IPR020103 all species →	Homologous_superfamily	Pseudouridine synthase, catalytic domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23127 all species →	CENTROMERE/MICROTUBULE BINDING PROTEIN CBF5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0000495 all species →	Biological Process	box H/ACA sno(s)RNA 3'-end processing	Interproscan
GO:0009982 all species →	Molecular Function	pseudouridine synthase activity	Interproscan
GO:0031118 all species →	Biological Process	rRNA pseudouridine synthesis	Interproscan
GO:0031120 all species →	Biological Process	snRNA pseudouridine synthesis	Interproscan
GO:0031429 all species →	Cellular Component	box H/ACA snoRNP complex	Interproscan
GO:1990481 all species →	Biological Process	mRNA pseudouridine synthesis	Interproscan
GO:0001522 all species →	Biological Process	pseudouridine synthesis	Interproscan
GO:0009451 all species →	Biological Process	RNA modification	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
K11131	DKC1, NOLA4, CBF5; H/ACA ribonucleoprotein complex subunit 4	EC:5.4.99.-	DNA replication proteins	ko03032	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_010276-T1 across 110 RNA-seq samples of Lophelia pertusa. 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.

110Samples

110TPM > 0

7Conditions

173.6Max TPM

58.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	56.86	73.54
polyp at pH7 6	18	18	68.95	173.55
coral polyp · control treatment	16	16	63.66	105.74
coral polyp · oil and dispersant treatment	16	16	44.82	72.93
coral polyp · oil treatment	16	16	54.74	96.21
coral polyp · dispersant treatment	16	16	49.74	124.61
Polyp	10	10	74.53	114.51

Per sample · hover a bar for the full sample record

Show the sample table (110 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	73.54
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.97
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.48
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.17
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.34
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.35
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.58
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.56
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.60
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.12
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.56
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.33
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.49
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.36
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	173.55
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	157.73
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.14
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.45
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.95
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.76
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.98
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.85
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.80
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.47
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.87
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.80
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.42
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.13
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.41
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.96
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.85
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.74
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	95.03
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.19
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.26
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.91
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.94
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.77
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.93
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.04
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.83
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.53
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.04
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.63
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.93
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.92
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.08
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.52
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.31
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.03
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.97
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.91
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.83
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.16
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.23
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.85
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.66
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.99
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.21
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.24
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.05
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.72
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.81
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.51
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.99
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.33
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.43
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.38
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.11
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.04
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.44
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.77
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	124.61
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	95.18
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.47
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.67
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.42
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.04
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.31
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.31
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.72
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.26
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.57
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.76
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.65
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	114.51
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	105.17
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	96.82
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	94.58
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	87.79
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	69.19
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	67.68
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	42.19
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	39.01
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	28.37

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 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 Lophelia pertusa 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	28	OS493_025426-T1	0.841598786628967
Negatively correlated	3	OS493_026665-T1	-0.44145655860252

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 Lophelia pertusa, 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 →