Gene detail

Detailed information of OS493_027713-T1 in Lophelia pertusa

Genomic Location: scaffold_153:237264...240774
NR annotation: KAJ7377636.1, U4/U6-U5 snRNP complex subunit lsm8 [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
Q3ZCE0	U6 snRNA-associated Sm-like protein LSm8 OS=Bos taurus OX=9913 GN=LSM8 PE=3 SV=3
O95777	U6 snRNA-associated Sm-like protein LSm8 OS=Homo sapiens OX=9606 GN=LSM8 PE=1 SV=3
Q6ZWM4	U6 snRNA-associated Sm-like protein LSm8 OS=Mus musculus OX=10090 GN=Lsm8 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002631 (this species only)

Pfam domain

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

InterPro

InterPro term	Type	Description	Source
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR044642 all species →	Family	U6 snRNA-associated Sm-like protein Lsm1/8	Interproscan
IPR034103 all species →	Domain	Sm-like protein Lsm8	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15588 all species →	LSM1	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:0005688 all species →	Cellular Component	U6 snRNP	Interproscan
GO:0016070 all species →	Biological Process	RNA metabolic process	Interproscan
GO:0046540 all species →	Cellular Component	U4/U6 x U5 tri-snRNP complex	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K12627	LSM8; U6 snRNA-associated Sm-like protein LSm8	-	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_027713-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

63.6Max TPM

16.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.73	36.31
polyp at pH7 6	18	18	21.36	36.57
coral polyp · control treatment	16	16	15.84	26.85
coral polyp · oil and dispersant treatment	16	16	11.38	17.60
coral polyp · oil treatment	16	16	15.78	26.40
coral polyp · dispersant treatment	16	16	8.95	25.65
Polyp	10	10	26.62	63.60

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	-	36.31
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.64
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.50
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.93
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.53
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.43
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.76
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.33
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.07
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.68
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.65
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.87
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.33
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.14
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.06
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.88
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.57
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.75
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.57
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.22
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.82
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.75
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.95
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.75
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.90
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.54
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.51
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.29
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.27
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.97
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.68
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.59
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.11
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.85
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.62
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.17
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.87
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.71
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.85
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.41
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.88
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.28
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.91
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.18
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.19
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.75
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.81
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.60
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.71
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.59
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.75
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.54
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.92
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.16
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.59
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.93
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.89
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.99
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.82
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.09
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.98
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.41
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.40
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.04
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.14
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.63
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.07
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.68
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.38
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.72
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.60
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.32
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.81
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.30
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.90
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.01
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.52
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.65
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.48
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.22
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.18
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.01
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.95
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.38
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.47
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.84
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.51
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.42
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.40
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.48
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.68
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.48
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	63.60
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	34.94
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	34.85
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	22.46
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	20.87
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	20.18
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	19.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.21
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.02
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.70

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.