Gene detail

Detailed information of OS493_015991-T1 in Lophelia pertusa

Genomic Location: scaffold_48:2320522...2325815
NR annotation: KAJ7333898.1, 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
P0CR16	Multiple RNA-binding domain-containing protein 1 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) OX=214684 GN=MRD1 PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003576 (this species only) · gene tree & orthology

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
IPR034423 all species →	Domain	Probable RNA-binding protein 19, RNA recognition motif 5	Interproscan
IPR034421 all species →	Domain	Probable RNA-binding protein 19, RNA recognition motif 6	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
PTHR10352 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT G	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_015991-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_015991-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

25.1Max TPM

11.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.29	23.48
polyp at pH7 6	18	18	16.14	25.07
coral polyp · control treatment	16	16	12.19	22.30
coral polyp · oil and dispersant treatment	16	16	7.58	15.07
coral polyp · oil treatment	16	16	10.16	14.17
coral polyp · dispersant treatment	16	16	6.04	17.09
Polyp	10	9	12.22	17.04

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.48
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.74
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.06
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.40
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.20
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.61
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.30
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.09
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.01
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.14
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.42
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.12
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.62
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.40
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.30
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.21
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.03
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.07
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.08
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.58
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.60
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.49
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.97
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.79
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.62
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.24
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.22
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.29
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.33
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.76
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.35
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.09
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.79
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.30
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.48
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.10
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.06
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.90
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.81
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.01
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.87
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.75
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.75
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.02
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.08
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.58
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.68
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.92
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.07
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.89
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.73
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.71
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.70
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.38
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.56
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.10
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.04
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.85
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.56
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.44
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.42
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.33
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.58
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.17
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.07
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.88
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.83
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.49
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.94
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.31
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.67
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.30
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.18
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.74
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.03
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.80
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.09
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.09
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.88
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.52
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.65
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.62
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.11
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.05
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.74
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.68
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.67
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.58
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.20
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.07
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.58
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.53
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	17.04
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	16.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.88
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	15.37
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	15.34
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	13.80
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.66
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.82
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.