Gene detail

Detailed information of OS493_004794-T1 in Lophelia pertusa

Genomic Location: scaffold_9:4886846...4889763
NR annotation: KAJ7381193.1, hypothetical protein OS493_004794 [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
A7SEP9	U1 small nuclear ribonucleoprotein C OS=Nematostella vectensis OX=45351 GN=v1g244745 PE=3 SV=1
Q7PXU6	U1 small nuclear ribonucleoprotein C OS=Anopheles gambiae OX=7165 GN=AGAP001584 PE=3 SV=2
E3X5D6	U1 small nuclear ribonucleoprotein C OS=Anopheles darlingi OX=43151 GN=AND_004369 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009143 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06220 all species →	zf-U1	U1 zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013085 all species →	Domain	U1-C, C2H2-type zinc finger	Interproscan
IPR017340 all species →	Family	U1 small nuclear ribonucleoprotein C	Interproscan
IPR036236 all species →	Homologous_superfamily	Zinc finger C2H2 superfamily	Interproscan
IPR003604 all species →	Domain	Matrin/U1-C-like, C2H2-type zinc finger	Interproscan
IPR000690 all species →	Domain	Matrin/U1-C, C2H2-type zinc finger	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR31148 all species →	U1 SMALL NUCLEAR RIBONUCLEOPROTEIN C	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0000387 all species →	Biological Process	spliceosomal snRNP assembly	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005685 all species →	Cellular Component	U1 snRNP	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000395 all species →	Biological Process	mRNA 5'-splice site recognition	Interproscan
GO:0030627 all species →	Molecular Function	pre-mRNA 5'-splice site binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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_004794-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_004794-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

97.5Max TPM

37.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	41.57	61.25
polyp at pH7 6	18	18	45.32	97.50
coral polyp · control treatment	16	16	40.08	72.37
coral polyp · oil and dispersant treatment	16	16	37.49	59.35
coral polyp · oil treatment	16	16	36.78	54.29
coral polyp · dispersant treatment	16	16	25.94	52.25
Polyp	10	10	34.67	68.73

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	-	61.25
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.73
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.21
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.16
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.96
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.47
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.25
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.21
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.88
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.89
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.21
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.94
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.73
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.70
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.61
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.75
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.68
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	97.50
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.35
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.72
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.82
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.03
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.66
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.56
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.89
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.34
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.29
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.54
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.24
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.64
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.42
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.49
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.09
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.54
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.72
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.37
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.23
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.33
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.77
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.54
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.42
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.20
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.05
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.88
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.53
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.20
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.94
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.69
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.13
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.32
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.89
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.75
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.07
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.31
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.56
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.23
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.13
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.92
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.84
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.99
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.71
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.29
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.86
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.13
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.29
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.92
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.87
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.81
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.86
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.42
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.99
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.26
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.90
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.45
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.25
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.90
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.86
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.89
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.98
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.88
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.25
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.89
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.13
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.02
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.01
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.06
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.74
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.66
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.05
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.01
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.92
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.31
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.83
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.35
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.24
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.56
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	68.73
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	56.97
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	42.90
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	36.89
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	34.69
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	34.26
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	25.10
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	19.18
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.07
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	12.88

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.