Gene detail

Detailed information of OS493_001103-T1 in Lophelia pertusa

Genomic Location: scaffold_2:4623024...4639418
NR annotation: KAJ7387760.1, poly(U) RNA binding [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
Q9WU01	KH domain-containing, RNA-binding, signal transduction-associated protein 2 OS=Mus musculus OX=10090 GN=Khdrbs2 PE=1 SV=1
Q5VWX1	KH domain-containing, RNA-binding, signal transduction-associated protein 2 OS=Homo sapiens OX=9606 GN=KHDRBS2 PE=1 SV=1
Q920F3	KH domain-containing, RNA-binding, signal transduction-associated protein 2 OS=Rattus norvegicus OX=10116 GN=Khdrbs2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001209 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16274 all species →	Qua1	Qua1 domain	Domain	Interproscan
PF00013 all species →	KH_1	KH domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036612 all species →	Homologous_superfamily	K Homology domain, type 1 superfamily	Interproscan
IPR032571 all species →	Domain	KHDRBS, Qua1 domain	Interproscan
IPR004087 all species →	Domain	K Homology domain	Interproscan
IPR004088 all species →	Domain	K Homology domain, type 1	Interproscan
IPR045071 all species →	Family	KH domain-containing BBP-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11208 all species →	RNA-BINDING PROTEIN RELATED	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
GO:0000381 all species →	Biological Process	regulation of alternative mRNA splicing, via spliceosome	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0048024 all species →	Biological Process	regulation of mRNA splicing, via spliceosome	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
K14942	KHDRBS3, SLM2; KH domain-containing, RNA-binding, signal transduction-associated protein 3	-	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_001103-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

111.0Max TPM

41.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	34.52	58.36
polyp at pH7 6	18	18	36.52	52.88
coral polyp · control treatment	16	16	45.27	106.11
coral polyp · oil and dispersant treatment	16	16	57.88	111.04
coral polyp · oil treatment	16	16	43.26	95.15
coral polyp · dispersant treatment	16	16	43.18	74.71
Polyp	10	10	22.08	33.58

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	-	58.36
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.03
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.50
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.23
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.69
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.56
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.01
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.08
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.30
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.13
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.68
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.71
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.59
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.18
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.08
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.44
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.70
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.08
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.88
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.03
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.84
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.70
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.73
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.65
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.34
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.43
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.68
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.07
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.68
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.45
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.68
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.32
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.05
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	106.11
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.95
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.63
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.96
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.73
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.13
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.71
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.75
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.08
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.48
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.34
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.98
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.69
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.62
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.73
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.04
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.70
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.17
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.52
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.38
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.81
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.55
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.62
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.05
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.94
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.79
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.63
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.83
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.13
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	95.15
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.40
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.38
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.08
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.88
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.61
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.36
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.60
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.01
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.15
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.04
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.02
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.11
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.85
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.40
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.09
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.71
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.49
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.90
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.85
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.01
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.71
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.83
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.19
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.92
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.05
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.41
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.03
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.65
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.04
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.10
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	33.58
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	31.82
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	31.04
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	28.51
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	24.79
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	23.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	17.60
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.57
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.95
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.68

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.