Gene detail

Detailed information of OS493_009893-T1 in Lophelia pertusa

Genomic Location: scaffold_24:533661...536556
NR annotation: KAJ7337043.1, Putative RNA-binding protein 18 [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
Q66J99	Probable RNA-binding protein 18 OS=Xenopus laevis OX=8355 GN=rbm18 PE=2 SV=1
Q96H35	Probable RNA-binding protein 18 OS=Homo sapiens OX=9606 GN=RBM18 PE=1 SV=1
Q9CR83	Probable RNA-binding protein 18 OS=Mus musculus OX=10090 GN=Rbm18 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009372 (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
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR039157 all species →	Domain	RNA-binding protein 18, RNA recognition motif	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21245 all species →	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K24527	RBM18; RNA-binding protein 18	-	Spliceosome	ko03041	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_009893-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

61.9Max TPM

12.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.83	12.13
polyp at pH7 6	18	18	11.08	18.04
coral polyp · control treatment	16	16	18.08	43.34
coral polyp · oil and dispersant treatment	16	16	16.45	61.86
coral polyp · oil treatment	16	16	15.52	21.84
coral polyp · dispersant treatment	16	16	6.84	13.31
Polyp	10	9	11.35	21.63

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.13
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.62
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.19
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.02
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.44
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.05
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.03
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.78
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.10
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.74
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.43
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.23
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.37
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.87
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.68
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.45
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.87
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.04
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.40
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.32
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.95
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.92
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.27
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.13
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.92
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.79
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.61
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.51
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.79
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.76
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.11
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.49
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.48
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.73
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.34
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.55
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.50
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.06
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.43
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.33
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.06
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.27
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.31
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.26
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.63
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.93
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.06
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.48
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.34
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.69
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.86
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.46
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.29
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.82
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.77
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.92
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.21
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.13
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.63
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.88
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.94
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.41
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.42
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.80
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.58
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.31
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.10
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.78
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.34
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.43
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.05
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.10
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.81
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.60
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.87
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.15
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.26
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.68
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.31
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.13
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.58
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.93
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.67
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.38
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.84
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.79
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.67
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.56
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.52
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.92
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.36
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.49
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.17
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.12
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	21.63
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.81
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.29
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.09
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.39
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.11
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.88
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.