Gene detail

Detailed information of OS493_015990-T1 in Lophelia pertusa

Genomic Location: scaffold_48:2316865...2319807
NR annotation: KAJ7333897.1, putative RNA-binding protein 19 [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
Q9Y4C8	Probable RNA-binding protein 19 OS=Homo sapiens OX=9606 GN=RBM19 PE=1 SV=3
Q8R3C6	Probable RNA-binding protein 19 OS=Mus musculus OX=10090 GN=Rbm19 PE=1 SV=1
Q54PB2	Multiple RNA-binding domain-containing protein 1 OS=Dictyostelium discoideum OX=44689 GN=mrd1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003543 (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
IPR051945 all species →	Family	RRM MRD1 RNA Processing and Ribosome Biogenesis	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
PTHR48039 all species →	RNA-BINDING MOTIF PROTEIN 14B	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA 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
K14787	MRD1, RBM19; multiple RNA-binding domain-containing protein 1	-	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_015990-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

12.0Max TPM

5.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.45	10.29
polyp at pH7 6	18	18	7.07	8.71
coral polyp · control treatment	16	16	6.53	9.99
coral polyp · oil and dispersant treatment	16	16	4.56	7.51
coral polyp · oil treatment	16	16	5.50	7.94
coral polyp · dispersant treatment	16	16	3.69	12.03
Polyp	10	10	5.32	8.12

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.29
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.66
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.27
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.31
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.07
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.99
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.82
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.29
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.13
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.06
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.99
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.94
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.30
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.68
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.49
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.24
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.71
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.47
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.27
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.25
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.03
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.47
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.03
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.83
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.81
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.62
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.60
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.16
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.10
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.06
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.70
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.99
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.96
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.78
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.70
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.45
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.28
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.01
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.63
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.51
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.68
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.45
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.25
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.74
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.54
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.87
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.70
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.51
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.48
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.23
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.62
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.33
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.09
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.07
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.03
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.71
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.49
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.32
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.94
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.57
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.34
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.94
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.88
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.18
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.69
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.67
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.92
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.61
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.40
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.16
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.03
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.70
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.60
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.09
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.73
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.55
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.03
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.17
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.58
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.56
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.16
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.63
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.51
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.31
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.29
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.92
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.40
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.37
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.58
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.16
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.42
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.12
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.74
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.54
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.17
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.35
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.31
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.63
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.36

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.