Gene detail

Detailed information of OS493_008235-T1 in Lophelia pertusa

Genomic Location: scaffold_19:1517120...1541099
NR annotation: KAJ7392989.1, pre-mRNA 3-end-processing factor fip1l1 [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
Q5XJD3	Pre-mRNA 3'-end-processing factor FIP1 OS=Danio rerio OX=7955 GN=fip1l1 PE=1 SV=1
Q5U317	Pre-mRNA 3'-end-processing factor FIP1 OS=Rattus norvegicus OX=10116 GN=Fip1l1 PE=1 SV=1
Q5RAA7	Pre-mRNA 3'-end-processing factor FIP1 OS=Pongo abelii OX=9601 GN=FIP1L1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004847 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05182 all species →	Fip1	Fip1 motif	Motif	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051187 all species →	Family	Pre-mRNA 3'-end-processing regulator	Interproscan
IPR007854 all species →	Domain	Pre-mRNA polyadenylation factor Fip1 domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13484 all species →	FIP1-LIKE 1 PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005847 all species →	Cellular Component	mRNA cleavage and polyadenylation specificity factor complex	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
K14405	FIP1L1, FIP1; pre-mRNA 3'-end-processing factor FIP1	-	Messenger RNA biogenesis	ko03019	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_008235-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

109TPM > 0

7Conditions

47.0Max TPM

18.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.54	27.74
polyp at pH7 6	18	18	17.82	26.16
coral polyp · control treatment	16	16	25.01	46.95
coral polyp · oil and dispersant treatment	16	16	18.25	31.97
coral polyp · oil treatment	16	16	22.07	38.78
coral polyp · dispersant treatment	16	16	15.52	34.75
Polyp	10	9	9.08	16.06

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	-	27.74
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.42
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.91
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.24
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.66
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.25
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.57
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.54
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.18
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.18
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.47
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.80
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.60
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.50
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.68
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.90
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.57
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.16
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.17
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.13
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.79
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.58
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.41
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.92
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.97
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.88
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.28
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.09
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.59
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.58
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.41
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.35
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.36
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.83
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.95
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.71
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.01
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.59
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.74
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.35
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.29
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.88
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.74
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.07
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.56
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.90
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.20
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.11
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.39
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.75
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.13
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.50
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.65
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.20
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.65
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.46
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.80
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.61
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.27
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.21
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.15
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.95
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.74
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.45
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.78
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.16
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.01
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.59
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.16
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.16
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.54
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.14
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.99
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.84
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.97
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.31
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.25
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.99
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.75
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.26
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.91
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.67
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.80
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.48
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.68
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.39
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.10
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.92
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.39
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.27
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.57
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.41
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.25
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.52
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	16.06
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	13.99
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.16
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.44
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.17
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.20
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.18
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.87
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.74
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.