Gene detail

Detailed information of OS493_006235-T1 in Lophelia pertusa

Genomic Location: scaffold_13:1265726...1266782
NR annotation: KAJ7393266.1, hypothetical protein OS493_006235 [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
Q62504	Msx2-interacting protein OS=Mus musculus OX=10090 GN=Spen PE=1 SV=2
Q96T58	Msx2-interacting protein OS=Homo sapiens OX=9606 GN=SPEN PE=1 SV=1
Q8SX83	Protein split ends OS=Drosophila melanogaster OX=7227 GN=spen PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002806 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07744 all species →	SPOC	SPOC domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR010912 all species →	Domain	Spen paralogue/orthologue C-terminal, metazoa	Interproscan
IPR016194 all species →	Homologous_superfamily	SPOC-like, C-terminal domain superfamily	Interproscan
IPR012921 all species →	Domain	Spen paralogue and orthologue SPOC, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23189 all species →	RNA RECOGNITION MOTIF-CONTAINING	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:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	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_006235-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_006235-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

83.4Max TPM

43.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	39.30	57.61
polyp at pH7 6	18	18	35.98	49.59
coral polyp · control treatment	16	16	53.67	64.75
coral polyp · oil and dispersant treatment	16	16	53.25	78.22
coral polyp · oil treatment	16	16	46.09	67.24
coral polyp · dispersant treatment	16	16	44.67	83.40
Polyp	10	10	24.37	31.47

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.89
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.33
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.75
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.71
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.56
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.92
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.42
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.75
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.55
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.03
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.86
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.49
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.30
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.88
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.49
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.59
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.57
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.37
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.99
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.95
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.41
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.19
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.10
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.09
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.49
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.71
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.13
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.09
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.81
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.80
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.18
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.75
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.73
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.22
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.60
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.05
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.09
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.37
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.51
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.05
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.73
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.98
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.06
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.92
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.41
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.46
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.75
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.22
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.90
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.25
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.09
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.28
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.33
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.79
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.69
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.86
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.57
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.96
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.18
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.24
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.12
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.61
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.63
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.71
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.49
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.87
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.04
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.08
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.61
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.96
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.29
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	83.40
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.58
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.40
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.85
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.34
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.54
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.74
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.48
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.25
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.74
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.07
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.92
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.00
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.66
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.26
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	31.47
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	30.85
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	28.95
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	28.78
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	25.85
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	23.38
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	22.52
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	20.40
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	17.36
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.16

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.