Gene detail

Detailed information of OS493_022523-T1 in Lophelia pertusa

Genomic Location: scaffold_93:854922...861160
NR annotation: KAJ7378539.1, Crooked neck-like protein 1 [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
P17886	Protein crooked neck OS=Drosophila melanogaster OX=7227 GN=crn PE=2 SV=2
Q4WT84	Pre-mRNA-splicing factor clf1 OS=Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) OX=330879 GN=clf1 PE=3 SV=1
Q5K654	Pre-mRNA-splicing factor CLF1 OS=Paracoccidioides brasiliensis OX=121759 GN=CLF1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004179 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for OS493_022523-T1 in Lophelia pertusa.

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR045075 all species →	Family	Pre-mRNA-splicing factor Syf1-like	Interproscan
IPR003107 all species →	Repeat	HAT (Half-A-TPR) repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11246 all species →	PRE-MRNA SPLICING FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000245 all species →	Biological Process	spliceosomal complex assembly	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000974 all species →	Cellular Component	Prp19 complex	Interproscan
GO:0071007 all species →	Cellular Component	U2-type catalytic step 2 spliceosome	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	Interproscan
GO:0071014 all species →	Cellular Component	post-mRNA release spliceosomal complex	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	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_022523-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_022523-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

77TPM > 0

7Conditions

17.4Max TPM

3.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	14	5.98	17.41
polyp at pH7 6	18	12	5.36	15.96
coral polyp · control treatment	16	12	2.15	5.28
coral polyp · oil and dispersant treatment	16	11	1.46	4.04
coral polyp · oil treatment	16	11	2.28	6.78
coral polyp · dispersant treatment	16	12	1.82	6.45
Polyp	10	5	1.13	3.96

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.41
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.33
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.80
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.30
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.15
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.38
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.15
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.76
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.55
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.95
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.43
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.07
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.76
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.64
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.96
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.91
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.66
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.05
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.91
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.12
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.94
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.19
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.18
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.58
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.28
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.16
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.81
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.61
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.43
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.68
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.43
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.04
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.50
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.20
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.04
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.75
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.53
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.28
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.17
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.52
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.36
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.13
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.04
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.78
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.86
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.55
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.95
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.77
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.57
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.98
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.55
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.38
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.07
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.43
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.02
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.53
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.25
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.99
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.80
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.78
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.94
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.76
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.77
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.83
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.27
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.