Gene detail

Detailed information of OS493_039696-T1 in Lophelia pertusa

Genomic Location: scaffold_1381:8141...10699
NR annotation: KAJ7388123.1, small nuclear ribonucleoprotein 35kDa (U11 U12) [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
Q1LZH0	U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Bos taurus OX=9913 GN=SNRNP35 PE=2 SV=1
Q16560	U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Homo sapiens OX=9606 GN=SNRNP35 PE=1 SV=1
Q5U1W5	U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Rattus norvegicus OX=10116 GN=Snrnp35 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002747 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR051183 all species →	Family	U1 snRNP 70 kDa and U11/U12 snRNP 35 kDa	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13952 all species →	U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KD	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:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005689 all species →	Cellular Component	U12-type spliceosomal complex	Interproscan
GO:0017069 all species →	Molecular Function	snRNA binding	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	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_039696-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_039696-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

105TPM > 0

7Conditions

11.2Max TPM

3.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.41	7.85
polyp at pH7 6	18	17	4.62	10.27
coral polyp · control treatment	16	16	3.01	7.21
coral polyp · oil and dispersant treatment	16	15	1.77	4.33
coral polyp · oil treatment	16	16	3.40	8.61
coral polyp · dispersant treatment	16	14	1.39	5.39
Polyp	10	9	4.29	11.24

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.85
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.38
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.35
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.73
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.58
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.51
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.46
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.84
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.30
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.81
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.71
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.69
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.04
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.01
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.60
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.21
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.27
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.66
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.88
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.84
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.54
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.30
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.58
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.62
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.29
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.22
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.33
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.15
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.55
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.49
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.45
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.20
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.21
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.05
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.77
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.13
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.68
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.10
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.48
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.34
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.20
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.86
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.69
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.44
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.41
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.36
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.12
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.33
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.12
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.98
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.90
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.12
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.95
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.65
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.63
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.60
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.90
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.81
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.77
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.65
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.37
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.61
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.38
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.36
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.64
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.67
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.63
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.67
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.65
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.46
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.96
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.86
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.58
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.32
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.01
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.78
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.39
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.09
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.46
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.23
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.14
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.09
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.71
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.67
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.61
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.58
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.50
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.28
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.24
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.78
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.01
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.49
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.69
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.03
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.88
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.86
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.93
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.