Gene detail

Detailed information of OS493_003614-T1 in Lophelia pertusa

Genomic Location: scaffold_7:3671957...3679014
NR annotation: KAJ7393945.1, RNA-binding protein with multiple splicing 2 [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
Q07655	Protein WHI4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=WHI4 PE=1 SV=1
Q01617	Protein couch potato OS=Drosophila melanogaster OX=7227 GN=cpo PE=2 SV=4
Q93062	RNA-binding protein with multiple splicing OS=Homo sapiens OX=9606 GN=RBPMS PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002509 (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
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10501 all species →	U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA 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_003614-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_003614-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

109TPM > 0

7Conditions

141.1Max TPM

24.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	35.97	81.91
polyp at pH7 6	18	18	15.82	29.99
coral polyp · control treatment	16	16	31.21	63.85
coral polyp · oil and dispersant treatment	16	15	13.85	48.18
coral polyp · oil treatment	16	16	22.13	73.38
coral polyp · dispersant treatment	16	16	17.29	69.46
Polyp	10	10	44.75	141.07

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	81.91
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.80
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.33
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.29
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.48
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.39
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.51
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.30
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.82
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.70
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.16
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.15
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.55
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.06
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.55
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.42
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.99
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.30
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.54
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.95
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.79
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.20
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.69
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.32
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.78
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.20
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.91
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.59
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.83
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.93
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.56
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.90
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.58
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.63
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.85
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.14
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.38
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.18
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.44
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.22
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.27
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.28
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.93
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.73
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.19
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.84
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.90
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.10
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.18
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.28
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.83
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.73
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.85
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.82
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.67
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.05
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.88
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.79
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.66
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.69
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.07
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.38
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.44
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.31
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.72
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.25
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.05
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.47
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.89
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.72
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.23
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.99
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.89
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.95
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.22
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.44
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.46
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.70
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.91
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.25
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.10
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.46
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.19
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.92
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.80
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.98
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.82
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.86
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.81
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	141.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	66.95
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	56.59
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	55.38
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	50.45
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	24.38
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	23.32
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.70
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	12.55
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.11

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.