Gene detail

Detailed information of OS493_009432-T1 in Lophelia pertusa

Genomic Location: scaffold_22:2790217...2794391
NR annotation: KAJ7374100.1, serine arginine-rich splicing factor [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
Q8VE97	Serine/arginine-rich splicing factor 4 OS=Mus musculus OX=10090 GN=Srsf4 PE=2 SV=1
Q08170	Serine/arginine-rich splicing factor 4 OS=Homo sapiens OX=9606 GN=SRSF4 PE=1 SV=2
P26686	Serine-arginine protein 55 OS=Drosophila melanogaster OX=7227 GN=B52 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000618 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48038 all species →	RIBONUCLEOPROTEIN RB97D	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	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
K12893	SRSF4_5_6, SFRS4_5_6; serine/arginine-rich splicing factor 4/5/6	-	Spliceosome	ko03041	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_009432-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

272.4Max TPM

113.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	114.87	200.79
polyp at pH7 6	18	18	120.81	240.61
coral polyp · control treatment	16	16	122.35	236.81
coral polyp · oil and dispersant treatment	16	16	103.39	240.12
coral polyp · oil treatment	16	16	116.68	272.36
coral polyp · dispersant treatment	16	16	84.12	119.40
Polyp	10	10	141.68	236.49

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	-	200.79
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	180.39
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	166.64
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	151.02
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	138.83
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	130.26
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	106.92
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	106.49
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	101.96
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	99.23
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	97.94
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	96.14
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	88.53
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	86.54
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	83.54
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	80.28
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.18
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	74.99
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	240.61
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	211.13
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	168.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	158.49
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	157.12
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	153.95
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	142.28
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	139.89
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	123.92
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	123.38
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.28
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.32
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	77.28
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.69
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.44
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.21
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.60
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.50
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	236.81
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	205.29
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	175.36
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	130.24
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	128.43
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	123.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	113.52
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	110.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	109.12
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	108.09
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.16
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.29
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.42
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.68
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.49
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.47
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	240.12
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	150.91
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	122.08
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	121.36
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	114.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.86
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	100.57
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.86
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.99
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.16
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.49
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	77.86
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.03
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.61
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.33
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.99
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	272.36
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	145.16
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	140.11
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	139.19
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	135.99
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	115.15
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	109.53
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	108.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.28
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	93.16
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.55
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	90.87
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	85.42
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.71
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.61
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.27
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.40
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	118.63
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	104.97
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	102.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	99.09
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	95.43
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.76
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.23
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.93
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.38
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.02
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.17
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.22
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	236.49
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	204.52
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	195.67
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	163.51
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	130.55
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	124.59
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	121.81
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	118.23
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	64.99
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	56.42

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.