Gene detail

Detailed information of OS493_003287-T1 in Lophelia pertusa

Genomic Location: scaffold_6:7366495...7374511
NR annotation: KAJ7340533.1, hypothetical protein OS493_003287 [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
O08583	THO complex subunit 4 OS=Mus musculus OX=10090 GN=Alyref PE=1 SV=3
Q3T0I4	THO complex subunit 4 OS=Bos taurus OX=9913 GN=ALYREF PE=2 SV=1
Q86V81	THO complex subunit 4 OS=Homo sapiens OX=9606 GN=ALYREF PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006966 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13865 all species →	FoP_duplication	C-terminal duplication domain of Friend of PRMT1	Family	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051229 all species →	Family	ALYREF mRNA export adapter	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR025715 all species →	Domain	Chromatin target of PRMT1 protein, C-terminal	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
PTHR19965 all species →	RNA AND EXPORT FACTOR BINDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006406 all species →	Biological Process	mRNA export from nucleus	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	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
K12881	THOC4, ALY; THO complex subunit 4	-	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_003287-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

207.2Max TPM

61.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	36.55	56.18
polyp at pH7 6	18	18	41.84	55.54
coral polyp · control treatment	16	16	84.72	137.92
coral polyp · oil and dispersant treatment	16	16	93.50	207.17
coral polyp · oil treatment	16	16	71.92	125.44
coral polyp · dispersant treatment	16	16	66.72	152.26
Polyp	10	10	26.48	51.61

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	-	56.18
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.87
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.49
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.07
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.91
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.64
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.50
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.35
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.81
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.58
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.31
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.76
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.22
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.58
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.28
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.83
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.16
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.43
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.54
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.18
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.12
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.59
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.07
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.84
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.68
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.08
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.97
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.07
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.63
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.88
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.46
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.25
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.61
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.46
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.52
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	137.92
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	134.15
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	126.41
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	95.48
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.36
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.87
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.37
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	89.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.67
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.86
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.97
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.27
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.92
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.65
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.09
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.02
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	207.17
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	122.67
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	122.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.90
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.17
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	105.01
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	99.78
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.09
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.46
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.21
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.07
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.44
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.80
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.88
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.84
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.56
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	125.44
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	117.60
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	110.35
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.78
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.10
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.38
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	74.43
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.34
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.22
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.09
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.36
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.21
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.57
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.45
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	152.26
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	124.25
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.65
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.81
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.44
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.99
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.38
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.92
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.76
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.47
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.90
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.97
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.20
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.98
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	51.61
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	35.21
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	33.31
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	30.27
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	29.07
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	22.57
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	20.91
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	15.08
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	15.02
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.79

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.