Gene detail

Detailed information of OS493_015628-T1 in Lophelia pertusa

Genomic Location: scaffold_47:1158776...1166420
NR annotation: KAJ7360526.1, RNA-binding protein 39 [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
Q5RC80	RNA-binding protein 39 OS=Pongo abelii OX=9601 GN=RBM39 PE=2 SV=1
Q14498	RNA-binding protein 39 OS=Homo sapiens OX=9606 GN=RBM39 PE=1 SV=2
Q8VH51	RNA-binding protein 39 OS=Mus musculus OX=10090 GN=Rbm39 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003797 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF15519 all species →	RBM39linker	linker between RRM2 and RRM3 domains in RBM39 protein	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
IPR006509 all species →	Family	Splicing factor, RBM39-like	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR029123 all species →	Domain	Splicing factor RBM39, linker	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48036 all species →	SPLICING FACTOR (PAD-1), PUTATIVE (AFU_ORTHOLOGUE AFUA_1G15810)-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:1990446 all species →	Molecular Function	U1 snRNP 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
K13091	RBM23_39; RNA-binding protein 23/39	-	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_015628-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

992.0Max TPM

396.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	436.67	633.41
polyp at pH7 6	18	18	410.15	570.33
coral polyp · control treatment	16	16	354.25	538.14
coral polyp · oil and dispersant treatment	16	16	359.24	484.44
coral polyp · oil treatment	16	16	385.67	683.77
coral polyp · dispersant treatment	16	16	299.18	532.32
Polyp	10	10	598.18	992.03

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	-	633.41
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	630.63
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	596.79
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	589.51
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	526.53
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	515.16
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	458.15
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	457.75
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	430.97
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	423.54
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	358.63
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	358.44
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	357.80
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	348.94
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	311.23
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	306.70
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	279.84
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	276.05
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	570.33
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	562.34
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	547.19
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	544.41
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	528.55
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	517.92
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	487.51
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	486.88
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	432.81
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	426.56
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	307.44
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	304.32
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	303.89
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	303.59
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	291.51
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	279.51
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	251.29
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	236.72
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	538.14
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	456.52
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	451.98
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	370.67
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	364.78
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	358.68
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	356.73
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	348.72
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	340.97
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	333.33
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	321.04
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	305.38
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	297.45
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	293.76
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	277.18
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	252.74
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	484.44
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	447.77
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	443.21
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	441.60
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	398.73
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	395.73
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	389.04
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	380.83
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	365.99
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	356.40
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	301.11
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	298.51
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	289.69
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	261.95
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	248.16
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	244.71
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	683.77
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	502.66
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	430.51
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	404.92
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	399.34
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	395.77
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	373.88
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	359.21
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	356.52
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	352.20
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	341.23
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	332.92
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	329.68
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	314.98
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	303.57
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	289.51
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	532.32
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	413.38
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	352.66
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	352.54
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	311.33
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	310.27
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	305.32
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	275.04
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	263.52
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	262.81
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	259.29
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	257.25
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	239.73
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	235.41
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	216.05
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	199.98
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	992.03
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	988.60
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	787.37
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	679.88
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	560.81
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	529.27
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	460.37
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	438.94
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	348.60
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	195.88

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.