Gene detail

Detailed information of OS493_024812-T1 in Lophelia pertusa

Genomic Location: scaffold_117:986855...993880
NR annotation: KAJ7378147.1, Pre-mRNA-splicing factor SYF1 [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
Q9HCS7	Pre-mRNA-splicing factor SYF1 OS=Homo sapiens OX=9606 GN=XAB2 PE=1 SV=2
Q9DCD2	Pre-mRNA-splicing factor SYF1 OS=Mus musculus OX=10090 GN=Xab2 PE=1 SV=1
Q99PK0	Pre-mRNA-splicing factor SYF1 OS=Rattus norvegicus OX=10116 GN=Xab2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005181 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for OS493_024812-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:0000349 all species →	Biological Process	generation of catalytic spliceosome for first transesterification step	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: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_024812-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_024812-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

60.4Max TPM

22.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	21.12	28.32
polyp at pH7 6	18	18	24.10	36.36
coral polyp · control treatment	16	16	24.18	50.87
coral polyp · oil and dispersant treatment	16	16	16.54	29.57
coral polyp · oil treatment	16	16	23.87	35.63
coral polyp · dispersant treatment	16	16	16.30	30.44
Polyp	10	10	38.64	60.40

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.32
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.30
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.46
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.76
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.24
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.07
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.76
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.69
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.97
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.92
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.86
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.85
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.50
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.77
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.48
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.22
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.36
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.53
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.38
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.93
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.61
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.21
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.98
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.04
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.48
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.29
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.83
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.49
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.69
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.91
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.38
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.20
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.69
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.74
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.87
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.54
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.46
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.58
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.81
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.94
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.52
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.27
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.43
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.36
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.16
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.76
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.38
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.46
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.57
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.71
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.61
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.44
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.05
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.41
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.39
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.06
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.36
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.92
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.73
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.74
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.90
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.63
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.83
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.19
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.72
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.43
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.84
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.53
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.24
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.79
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.88
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.24
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.19
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.18
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.96
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.83
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.44
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.23
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.76
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.50
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.50
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.01
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.12
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.01
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.84
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.62
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.84
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.95
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.21
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.08
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.22
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.47
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	60.40
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	48.92
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	41.96
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	39.84
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	37.85
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	35.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	34.67
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	33.46
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	28.23
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	25.80

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.