Gene detail

Detailed information of OS493_016502-T1 in Lophelia pertusa

Genomic Location: scaffold_50:2038354...2043049
NR annotation: KAJ7385418.1, RNA-binding protein 8A [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
Q3ZCE8	RNA-binding protein 8A OS=Bos taurus OX=9913 GN=RBM8A PE=2 SV=2
Q9Y5S9	RNA-binding protein 8A OS=Homo sapiens OX=9606 GN=RBM8A PE=1 SV=1
Q9CWZ3	RNA-binding protein 8A OS=Mus musculus OX=10090 GN=Rbm8a PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009310 (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
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR008111 all species →	Family	RNA-binding motif protein 8	Interproscan
IPR033744 all species →	Domain	RBM8, RNA recognition motif	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45894 all species →	RNA-BINDING PROTEIN 8A	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:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0008380 all species →	Biological Process	RNA splicing	Interproscan
GO:0035145 all species →	Cellular Component	exon-exon junction complex	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
K12876	RBM8A, Y14; RNA-binding protein 8A	-	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_016502-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

125.2Max TPM

58.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	54.76	64.81
polyp at pH7 6	18	18	55.67	72.78
coral polyp · control treatment	16	16	71.23	109.13
coral polyp · oil and dispersant treatment	16	16	54.84	84.02
coral polyp · oil treatment	16	16	63.30	97.25
coral polyp · dispersant treatment	16	16	50.96	125.18
Polyp	10	10	54.76	79.97

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.81
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.20
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.86
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.44
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.55
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.08
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.87
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.53
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.42
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.21
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.51
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.03
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.17
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.66
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.12
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.28
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.78
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.31
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.55
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.24
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.88
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.41
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.03
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.32
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.19
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.79
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.64
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.21
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.68
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.40
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.85
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.31
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.77
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	109.13
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.98
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.87
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.24
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.16
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.11
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.63
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.94
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.46
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.39
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.99
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.80
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.45
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.57
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.63
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.28
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.02
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.90
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.56
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.99
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.89
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.30
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.12
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.91
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.54
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.31
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.01
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.89
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.81
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.25
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.41
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.43
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	86.89
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.71
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.80
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.38
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.90
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.50
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.86
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.31
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.33
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.57
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.44
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.42
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	125.18
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.21
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.73
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.30
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.86
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.79
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.71
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.75
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.53
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.91
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.26
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.94
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.84
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.88
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	79.97
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	77.31
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	71.37
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	55.38
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	54.10
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	51.22
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	45.99
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	44.45
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	37.70
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	30.13

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.