Gene detail

Detailed information of OS493_000044-T1 in Lophelia pertusa

Genomic Location: scaffold_1:472688...482817
NR annotation: KAJ7394242.1, Serine/arginine repetitive matrix 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
Q52KI8	Serine/arginine repetitive matrix protein 1 OS=Mus musculus OX=10090 GN=Srrm1 PE=1 SV=2
Q8IYB3	Serine/arginine repetitive matrix protein 1 OS=Homo sapiens OX=9606 GN=SRRM1 PE=1 SV=2
Q5R5Q2	Serine/arginine repetitive matrix protein 1 OS=Pongo abelii OX=9601 GN=SRRM1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001370 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13472 all species →	Lipase_GDSL_2	GDSL-like Lipase/Acylhydrolase family	Domain	Interproscan
PF01480 all species →	PWI	PWI domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002483 all species →	Domain	PWI domain	Interproscan
IPR036483 all species →	Homologous_superfamily	PWI domain superfamily	Interproscan
IPR013830 all species →	Domain	SGNH hydrolase-type esterase domain	Interproscan
IPR052225 all species →	Family	Serine/arginine repetitive matrix	Interproscan
IPR036514 all species →	Homologous_superfamily	SGNH hydrolase superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23148 all species →	SERINE/ARGININE REGULATED NUCLEAR MATRIX PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	Interproscan
GO:0048024 all species →	Biological Process	regulation of mRNA splicing, via spliceosome	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_000044-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_000044-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

66.8Max TPM

22.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.38	24.22
polyp at pH7 6	18	18	17.27	24.91
coral polyp · control treatment	16	16	29.63	45.79
coral polyp · oil and dispersant treatment	16	16	31.45	66.83
coral polyp · oil treatment	16	16	22.47	44.86
coral polyp · dispersant treatment	16	16	24.56	47.43
Polyp	10	10	9.38	13.85

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.22
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.09
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.19
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.99
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.54
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.79
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.14
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.28
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.55
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.42
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.38
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.97
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.70
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.58
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.83
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.75
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.29
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.06
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.91
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.73
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.45
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.20
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.88
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.59
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.97
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.45
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.72
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.56
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.39
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.19
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.73
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.69
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.67
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.71
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.46
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.52
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.79
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.84
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.07
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.51
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.47
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.55
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.76
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.85
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.56
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.42
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.81
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.28
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.79
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.92
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.13
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.32
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.83
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.54
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.63
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.20
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.16
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.09
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.90
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.64
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.64
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.82
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.72
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.46
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.76
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.40
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.37
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.86
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.65
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.06
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.57
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.25
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.66
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.32
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.17
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.96
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.06
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.52
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.17
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.37
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.73
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.43
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.91
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.92
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.99
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.10
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.53
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.17
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.55
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.38
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.78
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.88
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.33
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.60
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.01
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.61
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.71
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	13.85
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.76
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.52
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.68
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	10.36
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.91
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.69
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.76
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.42
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.82

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.