Gene detail

Detailed information of OS493_025214-T1 in Lophelia pertusa

Genomic Location: scaffold_122:292868...299417
NR annotation: KAJ7383890.1, hypothetical protein OS493_025214 [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
Q3T0Z8	Small nuclear ribonucleoprotein F OS=Bos taurus OX=9913 GN=SNRPF PE=3 SV=2
P62306	Small nuclear ribonucleoprotein F OS=Homo sapiens OX=9606 GN=SNRPF PE=1 SV=1
P62307	Small nuclear ribonucleoprotein F OS=Mus musculus OX=10090 GN=Snrpf PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002962 (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
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR034100 all species →	Family	Small nuclear ribonucleoprotein F	Interproscan
IPR016487 all species →	Family	Sm-like protein Lsm6/SmF	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11021 all species →	SMALL NUCLEAR RIBONUCLEOPROTEIN F SNRNP-F	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000387 all species →	Biological Process	spliceosomal snRNP assembly	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005685 all species →	Cellular Component	U1 snRNP	Interproscan
GO:0034715 all species →	Cellular Component	pICln-Sm protein complex	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 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
K11098	SNRPF, SMF; small nuclear ribonucleoprotein F	-	DNA replication proteins	ko03032	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_025214-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

209.1Max TPM

66.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	57.38	86.37
polyp at pH7 6	18	18	72.04	129.89
coral polyp · control treatment	16	16	77.52	209.12
coral polyp · oil and dispersant treatment	16	16	73.91	188.60
coral polyp · oil treatment	16	16	64.29	121.83
coral polyp · dispersant treatment	16	16	57.24	123.59
Polyp	10	10	63.78	143.67

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	-	86.37
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	85.68
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	71.46
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.20
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	67.66
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	67.28
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.89
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.60
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.00
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.13
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.53
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.28
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.89
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.13
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.16
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.26
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.72
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	129.89
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	127.83
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	122.61
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	116.96
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.99
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.72
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.41
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.88
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.23
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.35
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.06
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.63
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.85
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.76
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.02
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.74
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.81
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	209.12
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	107.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.61
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.33
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.79
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	88.15
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.18
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.73
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.31
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.62
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.50
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.18
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.15
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.52
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.30
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	188.60
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.77
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.04
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.74
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.80
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.83
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.67
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.28
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.02
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.85
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.13
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.68
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.08
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.96
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.88
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.83
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	89.17
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	87.42
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	84.78
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.42
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.71
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.43
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.62
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.08
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.55
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.08
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.01
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.66
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.01
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.95
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	123.59
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.01
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.79
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.36
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.57
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.70
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.20
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.93
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.97
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.05
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.45
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.86
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.99
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.11
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	143.67
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	92.43
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	82.55
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	68.66
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	57.86
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	55.02
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	47.88
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	43.62
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	23.38
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	22.74

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.