Gene detail

Detailed information of OS493_024818-T1 in Lophelia pertusa

Genomic Location: scaffold_117:1036580...1038822
NR annotation: KAJ7378153.1, U6 snRNA-associated Sm-like protein LSm2 [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
Q9Y333	U6 snRNA-associated Sm-like protein LSm2 OS=Homo sapiens OX=9606 GN=LSM2 PE=1 SV=1
O35900	U6 snRNA-associated Sm-like protein LSm2 OS=Mus musculus OX=10090 GN=Lsm2 PE=1 SV=1
Q54TF6	Probable U6 snRNA-associated Sm-like protein LSm2 OS=Dictyostelium discoideum OX=44689 GN=lsm2 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009651 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01423 all species →	LSM	LSM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR016654 all species →	Family	U6 snRNA-associated Sm-like protein LSm2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13829 all species →	SNRNP CORE PROTEIN FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0005688 all species →	Cellular Component	U6 snRNP	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:0046540 all species →	Cellular Component	U4/U6 x U5 tri-snRNP complex	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 spliceosome	Interproscan
GO:1990726 all species →	Cellular Component	Lsm1-7-Pat1 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
K12621	LSM2; U6 snRNA-associated Sm-like protein LSm2	-	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_024818-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

48.1Max TPM

21.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	23.48	39.72
polyp at pH7 6	18	17	23.97	38.10
coral polyp · control treatment	16	16	24.92	48.10
coral polyp · oil and dispersant treatment	16	16	17.07	46.25
coral polyp · oil treatment	16	16	22.08	32.46
coral polyp · dispersant treatment	16	16	14.81	30.09
Polyp	10	10	23.31	43.19

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.72
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.50
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.88
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.55
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.90
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.98
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.82
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.30
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.49
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.26
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.64
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.99
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.50
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.01
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.79
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.50
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.09
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.78
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.10
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.69
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.13
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.15
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.67
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.92
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.01
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.47
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.57
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.40
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.70
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.50
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.29
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.06
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.89
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.53
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.39
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.10
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.05
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.12
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.32
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.17
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.23
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.82
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.92
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.53
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.01
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.07
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.42
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.25
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.63
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.06
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.95
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.03
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.96
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.08
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.01
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.68
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.65
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.50
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.52
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.84
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.96
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.80
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.12
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.46
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.90
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.19
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.86
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.53
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.67
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.66
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.64
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.54
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.54
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.27
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.40
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.99
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.09
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.82
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.34
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.51
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.18
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.43
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.21
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.12
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.60
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.26
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.15
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.30
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.25
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.84
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.76
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	43.19
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	32.95
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	26.38
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	22.60
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	22.60
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	19.98
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.73
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	17.31
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	15.66
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.70

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.