Gene detail

Detailed information of OS493_024813-T1 in Lophelia pertusa

Genomic Location: scaffold_117:994018...1001783
NR annotation: KAJ7378148.1, 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_024813-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_024813-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_024813-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

40.3Max TPM

12.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.79	14.07
polyp at pH7 6	18	18	11.26	16.15
coral polyp · control treatment	16	16	16.43	40.26
coral polyp · oil and dispersant treatment	16	16	11.61	27.25
coral polyp · oil treatment	16	16	14.23	28.98
coral polyp · dispersant treatment	16	16	11.02	21.01
Polyp	10	9	9.92	17.73

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	-	14.07
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.28
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.25
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.17
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.90
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.78
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.15
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.21
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.68
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.25
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.21
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.17
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.17
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.99
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.30
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.04
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.83
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.15
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.90
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.57
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.18
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.76
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.33
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.08
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.01
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.92
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.66
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.51
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.40
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.06
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.03
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.38
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.12
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.24
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.33
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.26
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.29
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.92
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.42
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.53
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.23
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.74
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.40
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.35
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.07
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.70
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.61
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.59
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.78
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.25
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.75
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.52
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.42
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.56
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.71
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.70
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.97
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.60
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.33
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.35
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.50
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.24
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.50
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.98
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.56
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.41
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.47
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.05
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.94
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.78
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.05
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.92
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.50
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.03
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.15
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.87
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.82
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.42
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.01
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.77
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.73
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.29
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.72
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.26
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.23
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.79
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.07
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.44
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.81
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.28
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.49
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.78
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	17.73
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	15.92
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.70
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.61
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.90
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.10
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.68
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.68
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.