Gene detail

Detailed information of OS493_031251-T1 in Lophelia pertusa

Genomic Location: scaffold_213:196814...198882
NR annotation: KAJ7376979.1, SM-like, degradation of cytoplasmic mRNAs and positively regulates transcription initiation [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
Q8VC85	U6 snRNA-associated Sm-like protein LSm1 OS=Mus musculus OX=10090 GN=Lsm1 PE=1 SV=1
Q5E9Z8	U6 snRNA-associated Sm-like protein LSm1 OS=Bos taurus OX=9913 GN=LSM1 PE=2 SV=1
O15116	U6 snRNA-associated Sm-like protein LSm1 OS=Homo sapiens OX=9606 GN=LSM1 PE=1 SV=1

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
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan
IPR034104 all species →	Domain	Sm-like protein Lsm1	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR044642 all species →	Family	U6 snRNA-associated Sm-like protein Lsm1/8	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15588 all species →	LSM1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000956 all species →	Biological Process	nuclear-transcribed mRNA catabolic process	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000290 all species →	Biological Process	deadenylation-dependent decapping of nuclear-transcribed mRNA	Interproscan
GO:0000339 all species →	Molecular Function	RNA cap binding	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0016070 all species →	Biological Process	RNA metabolic process	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
K12620	LSM1; U6 snRNA-associated Sm-like protein LSm1	-	Messenger RNA biogenesis	ko03019	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_031251-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

116.3Max TPM

34.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	33.66	49.20
polyp at pH7 6	18	18	36.91	53.46
coral polyp · control treatment	16	16	44.98	116.33
coral polyp · oil and dispersant treatment	16	16	32.87	77.82
coral polyp · oil treatment	16	16	38.75	51.38
coral polyp · dispersant treatment	16	16	18.69	32.46
Polyp	10	10	33.20	57.41

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.20
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.92
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.82
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.62
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.85
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.06
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.72
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.43
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.11
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.57
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.14
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.73
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.39
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.38
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.32
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.94
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.56
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.04
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.46
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.21
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.08
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.50
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.98
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.83
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.13
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.23
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.59
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.29
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.90
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.33
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.53
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.32
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.58
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.50
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.99
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.97
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	116.33
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.53
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.14
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.01
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.52
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.14
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.07
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.24
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.03
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.50
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.24
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.00
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.48
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.59
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.49
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	77.82
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.74
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.46
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.43
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.06
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.77
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.39
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.35
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.86
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.59
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.51
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.27
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.13
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.54
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.78
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.38
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.37
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.18
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.56
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.48
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.98
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.39
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.22
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.75
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.59
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.29
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.88
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.64
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.13
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.17
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.46
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.69
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.92
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.41
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.07
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.72
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.47
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.21
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.54
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.40
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.14
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.37
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.41
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	57.41
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	39.94
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	37.21
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	35.10
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	34.33
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	33.06
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	29.94
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	28.46
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	19.85
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.69

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.