Gene detail

Detailed information of OS493_037311-T1 in Lophelia pertusa

Genomic Location: scaffold_416:170507...178467
NR annotation: KAJ7382077.1, hypothetical protein OS493_037311 [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
P20397	Nucleolin OS=Xenopus laevis OX=8355 GN=ncl PE=2 SV=3
P08199	Nucleolin OS=Mesocricetus auratus OX=10036 GN=NCL PE=1 SV=2
P13383	Nucleolin OS=Rattus norvegicus OX=10116 GN=Ncl PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004269 (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
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding 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: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

No KEGG orthology assignment for OS493_037311-T1.

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_037311-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

193.4Max TPM

59.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	37.18	61.28
polyp at pH7 6	18	18	53.06	95.08
coral polyp · control treatment	16	16	77.65	135.72
coral polyp · oil and dispersant treatment	16	16	73.36	158.62
coral polyp · oil treatment	16	16	53.25	120.74
coral polyp · dispersant treatment	16	16	85.73	193.41
Polyp	10	10	31.05	69.43

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.28
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.59
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.93
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.66
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.93
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.40
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.75
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.38
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.93
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.48
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.22
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.94
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.22
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.64
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.27
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.61
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.08
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	95.08
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	85.79
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.72
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.94
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.45
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.04
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.43
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.53
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.67
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.20
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.68
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.13
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.86
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.79
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.96
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	135.72
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.17
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	125.48
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	95.72
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	95.03
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.55
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.37
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.67
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.11
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.49
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.90
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.99
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.66
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.57
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	158.62
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	116.33
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	113.17
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.10
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	93.05
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.51
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.15
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.24
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.99
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.96
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.10
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.38
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.81
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.77
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.82
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	120.74
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	82.35
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.84
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.59
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.65
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.23
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.28
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.21
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.85
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.33
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.08
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.84
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.91
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.38
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	193.41
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	141.52
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.30
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	115.43
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	105.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	98.06
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	93.43
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	92.09
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.72
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.44
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.24
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.75
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.13
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.59
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.80
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.62
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	69.43
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	54.92
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	37.88
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	31.77
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	26.24
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	23.92
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	17.96
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.94
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	13.40

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.