Gene detail

Detailed information of OS493_027542-T1 in Lophelia pertusa

Genomic Location: scaffold_151:60349...64143
NR annotation: KAJ7390018.1, hypothetical protein OS493_027542 [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
Q9Y7Y3	Uncharacterized RNA-binding protein C365.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPBC365.04c PE=4 SV=1
Q07623	Nucleolar protein 6 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=NOP6 PE=1 SV=1
Q6Z1C0	Nucleolin 1 OS=Oryza sativa subsp. japonica OX=39947 GN=Os08g0192900 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009903 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR034228 all species →	Domain	Nop6, RNA recognition motif	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23236 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0019843 all species →	Molecular Function	rRNA binding	Interproscan
GO:0042274 all species →	Biological Process	ribosomal small subunit biogenesis	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid 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
K14789	NOP6; nucleolar protein 6	-	Ribosome biogenesis	ko03009	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_027542-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

108TPM > 0

7Conditions

30.2Max TPM

9.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.58	13.98
polyp at pH7 6	18	18	11.86	20.14
coral polyp · control treatment	16	16	10.48	19.29
coral polyp · oil and dispersant treatment	16	15	7.33	12.98
coral polyp · oil treatment	16	16	9.64	15.82
coral polyp · dispersant treatment	16	16	5.70	13.39
Polyp	10	9	10.54	30.16

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.98
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.82
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.65
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.52
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.67
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.94
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.81
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.44
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.44
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.66
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.40
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.84
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.74
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.70
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.57
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.14
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.18
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.14
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.34
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.93
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.53
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.37
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.98
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.54
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.29
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.23
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.92
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.31
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.18
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.33
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.06
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.29
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.18
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.32
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.37
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.66
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.62
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.80
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.25
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.21
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.37
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.56
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.46
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.10
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.40
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.08
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.98
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.41
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.14
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.12
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.56
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.66
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.51
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.22
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.75
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.02
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.97
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.87
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.86
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.82
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.69
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.73
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.99
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.92
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.56
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.50
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.97
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.50
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.23
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.11
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.55
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.54
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.36
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.14
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.58
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.51
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.29
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.10
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.08
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.03
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.07
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.06
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.15
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.95
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.92
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.88
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.47
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.92
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	30.16
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.94
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.58
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	11.52
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.38
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.47
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	9.36
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.26
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.70
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.