Gene detail

Detailed information of OS493_029435-T1 in Lophelia pertusa

Genomic Location: scaffold_179:229122...232434
NR annotation: KAJ7354878.1, U4/U6-U5 snRNP complex subunit lsm3 [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
Q32PE9	U6 snRNA-associated Sm-like protein LSm3 OS=Bos taurus OX=9913 GN=LSM3 PE=3 SV=3
P62310	U6 snRNA-associated Sm-like protein LSm3 OS=Homo sapiens OX=9606 GN=LSM3 PE=1 SV=2
P62311	U6 snRNA-associated Sm-like protein LSm3 OS=Mus musculus OX=10090 GN=Lsm3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009089 (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
IPR034105 all species →	Domain	Sm-like protein Lsm3	Interproscan
IPR040002 all species →	Family	U6 snRNA-associated Sm-like protein Lsm3	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13110 all species →	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3	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:0033962 all species →	Biological Process	P-body assembly	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
K12622	LSM3; U6 snRNA-associated Sm-like protein LSm3	-	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_029435-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

108.0Max TPM

45.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	48.28	77.06
polyp at pH7 6	18	18	51.69	83.76
coral polyp · control treatment	16	16	47.82	107.99
coral polyp · oil and dispersant treatment	16	16	34.26	76.75
coral polyp · oil treatment	16	16	43.95	73.90
coral polyp · dispersant treatment	16	16	26.91	53.48
Polyp	10	10	74.71	104.30

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	-	77.06
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.16
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.12
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.75
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.99
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.27
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.78
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.54
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.51
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.30
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.19
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.71
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.57
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.48
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.82
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.32
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.19
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.27
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	83.76
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.43
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.51
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.71
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.03
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.06
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.21
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.89
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.18
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.52
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.94
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.28
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.52
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.78
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.65
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.87
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.19
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	107.99
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.80
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.33
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.61
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.12
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.05
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.73
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.98
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.65
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.03
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.00
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.41
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.47
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.75
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.07
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.95
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.08
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.67
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.41
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.81
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.64
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.89
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.92
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.98
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.42
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.09
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.28
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.02
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.12
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.90
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.11
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.45
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.64
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.54
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.52
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.80
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.41
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.37
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.97
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.41
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.99
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.32
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.58
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.24
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.48
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.45
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.85
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.10
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.44
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.36
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.22
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.63
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.39
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.93
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.01
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.71
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.53
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.92
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	104.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	97.44
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	96.45
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	93.17
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	83.15
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	60.94
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	59.62
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	54.37
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	49.60
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	48.01

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.