Gene detail

Detailed information of OS493_002903-T1 in Lophelia pertusa

Genomic Location: scaffold_6:2044203...2047913
NR annotation: KAJ7340174.1, NHP2-like protein 1 [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
Q6P8E9	NHP2-like protein 1 OS=Xenopus tropicalis OX=8364 GN=snu13 PE=2 SV=1
Q5XH16	NHP2-like protein 1 OS=Xenopus laevis OX=8355 GN=snu13 PE=2 SV=1
Q3B8S0	NHP2-like protein 1 OS=Bos taurus OX=9913 GN=SNU13 PE=2 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008937 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01248 all species →	Ribosomal_L7Ae	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002415 all species →	Family	H/ACA ribonucleoprotein complex, subunit Nhp2-like	Interproscan
IPR029064 all species →	Homologous_superfamily	Ribosomal protein eL30-like superfamily	Interproscan
IPR004037 all species →	Conserved_site	Large ribosomal subunit protein eL8-like, conserved site	Interproscan
IPR050257 all species →	Family	Eukaryotic ribosomal RNA-processing and assembly protein	Interproscan
IPR018492 all species →	Family	Ribosomal protein eL8/Nhp2 family	Interproscan
IPR004038 all species →	Domain	Ribosomal protein eL8/eL30/eS12/Gadd45	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23105 all species →	RIBOSOMAL PROTEIN L7AE FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0042254 all species →	Biological Process	ribosome biogenesis	Interproscan
GO:1990904 all species →	Cellular Component	ribonucleoprotein complex	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000470 all species →	Biological Process	maturation of LSU-rRNA	Interproscan
GO:0022625 all species →	Cellular Component	cytosolic large ribosomal subunit	Interproscan
GO:0030490 all species →	Biological Process	maturation of SSU-rRNA	Interproscan
GO:0031428 all species →	Cellular Component	box C/D methylation guide snoRNP complex	Interproscan
GO:0032040 all species →	Cellular Component	small-subunit processome	Interproscan
GO:0046540 all species →	Cellular Component	U4/U6 x U5 tri-snRNP complex	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic 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
K12845	SNU13, NHP2L; U4/U6 small nuclear ribonucleoprotein SNU13	-	Ribosome biogenesis	ko03009	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_002903-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

380.7Max TPM

75.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	87.49	125.91
polyp at pH7 6	18	18	105.13	187.49
coral polyp · control treatment	16	16	57.82	105.35
coral polyp · oil and dispersant treatment	16	16	47.69	93.97
coral polyp · oil treatment	16	16	51.30	108.21
coral polyp · dispersant treatment	16	16	45.91	115.00
Polyp	10	10	160.38	380.65

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	-	125.91
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	121.30
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	120.62
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	110.35
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	104.67
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	98.76
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	94.56
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	87.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	85.76
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	84.86
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.85
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.38
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	76.36
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.47
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	74.59
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.90
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.42
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.01
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	187.49
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	164.85
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	162.24
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	159.89
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	113.16
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.53
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	108.26
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	107.34
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	99.28
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	97.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	95.52
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	94.49
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.76
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.38
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.97
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.82
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.42
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.69
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.35
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	95.18
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.54
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.19
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.50
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.48
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.42
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.28
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.57
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.26
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.24
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.36
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.02
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.63
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	93.97
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.06
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.16
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.47
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.94
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.98
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.32
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.40
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.99
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.98
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.87
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.85
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.94
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.18
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.17
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	108.21
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.85
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.61
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.19
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.97
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.11
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.25
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.69
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.67
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.17
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.16
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.60
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.36
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.15
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.38
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.39
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	115.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	83.97
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.44
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.64
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.48
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.37
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.63
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.76
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.50
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.87
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.75
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.87
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.77
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.68
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.56
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.21
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	380.65
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	250.06
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	203.42
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	195.93
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	179.23
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	112.34
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	108.45
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	60.82
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	60.68
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	52.19

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.