Gene detail

Detailed information of OS493_038403-T1 in Lophelia pertusa

Genomic Location: scaffold_575:48034...52584
NR annotation: KAJ7350117.1, hypothetical protein OS493_038403 [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
A0A0D1C8Z4	Glycine-rich RNA-binding protein 1 OS=Mycosarcoma maydis OX=5270 GN=GRP1 PE=1 SV=1
O89086	RNA-binding protein 3 OS=Mus musculus OX=10090 GN=Rbm3 PE=1 SV=1
W8E7I1	RNA-binding protein 3 OS=Capra hircus OX=9925 GN=RBM3 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009808 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF02213 all species →	GYF	GYF domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR003169 all species →	Domain	GYF domain	Interproscan
IPR050441 all species →	Family	RNA-binding motif	Interproscan
IPR035445 all species →	Homologous_superfamily	GYF-like domain superfamily	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
PTHR48034 all species →	TRANSFORMER-2 SEX-DETERMINING PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	Interproscan
GO:0048026 all species →	Biological Process	positive regulation of mRNA splicing, via spliceosome	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_038403-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_038403-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

65.0Max TPM

15.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	15.00	21.98
polyp at pH7 6	18	18	16.36	33.52
coral polyp · control treatment	16	16	17.96	50.43
coral polyp · oil and dispersant treatment	16	16	13.15	38.50
coral polyp · oil treatment	16	16	18.57	64.99
coral polyp · dispersant treatment	16	16	6.72	23.34
Polyp	10	10	20.00	33.07

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	-	21.98
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.36
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.41
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.17
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.13
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.40
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.16
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.17
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.11
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.96
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.41
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.18
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.09
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.96
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.71
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.52
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.33
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.14
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.80
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.78
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.71
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.63
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.83
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.54
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.48
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.64
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.92
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.53
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.41
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.46
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.38
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.25
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.43
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.31
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.50
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.76
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.71
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.18
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.03
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.69
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.43
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.02
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.52
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.22
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.58
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.22
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.06
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.50
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.39
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.07
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.61
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.12
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.63
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.81
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.03
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.02
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.07
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.15
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.76
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.31
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.09
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.79
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.99
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.27
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.78
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.40
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.20
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.70
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.64
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.22
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.40
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.51
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.50
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.46
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.56
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.27
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.34
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.03
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.59
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.37
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.52
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.75
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.24
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.34
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.80
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.57
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.51
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.17
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.94
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	33.07
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	27.34
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	25.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	21.58
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	20.58
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	18.18
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.98
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.96
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.24
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	8.84

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.