Gene detail

Detailed information of OS493_005026-T1 in Lophelia pertusa

Genomic Location: scaffold_10:2027759...2028456
NR annotation: KAJ7374684.1, RNA-binding protein 14 [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
Q8VE92	RNA-binding protein 4B OS=Mus musculus OX=10090 GN=Rbm4b PE=1 SV=1
Q64LC9	RNA-binding protein 4B OS=Rattus norvegicus OX=10116 GN=Rbm4b PE=2 SV=2
Q9BQ04	RNA-binding protein 4B OS=Homo sapiens OX=9606 GN=RBM4B PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002199 (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
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
PTHR21245 all species →	HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN	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: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_005026-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_005026-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

138.0Max TPM

67.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	54.15	68.15
polyp at pH7 6	18	18	57.47	78.27
coral polyp · control treatment	16	16	90.54	118.68
coral polyp · oil and dispersant treatment	16	16	79.01	137.98
coral polyp · oil treatment	16	16	81.55	116.38
coral polyp · dispersant treatment	16	16	64.46	115.44
Polyp	10	10	40.49	67.25

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	-	68.15
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.44
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.32
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.91
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.97
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.61
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.33
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.82
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.56
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.52
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.40
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.39
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.91
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.74
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.13
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.17
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.72
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.27
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.08
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.82
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.51
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.49
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.45
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.32
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.97
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.86
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.84
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.22
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.17
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.30
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.57
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.53
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.65
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.19
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	118.68
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	114.53
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	111.04
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	109.03
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	108.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.28
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.05
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.97
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.93
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.93
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.44
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	84.09
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.67
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.38
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.73
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	137.98
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	92.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.98
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.17
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.80
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.45
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.04
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.64
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.98
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	77.72
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.95
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.57
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.01
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.88
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	116.38
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	105.90
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.60
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.60
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	98.96
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	98.68
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.25
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	88.58
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.43
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.81
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.77
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.95
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.40
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.85
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.59
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	115.44
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	111.63
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	80.52
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.13
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.83
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.43
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.41
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.72
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.16
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.98
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.81
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.25
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.62
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.81
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.05
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.58
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	67.25
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	53.78
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	45.12
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	43.81
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	40.88
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	40.61
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	32.25
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	29.98
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	27.64
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	23.55

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.