Gene detail

Detailed information of OS493_035601-T1 in Lophelia pertusa

Genomic Location: scaffold_326:115561...124163
NR annotation: KAJ7382324.1, Nudix hydrolase 21, chloroplastic [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
Q6DJE4	Cleavage and polyadenylation specificity factor subunit 5 OS=Xenopus laevis OX=8355 GN=nudt21 PE=2 SV=1
Q3ZCA2	Cleavage and polyadenylation specificity factor subunit 5 OS=Bos taurus OX=9913 GN=NUDT21 PE=2 SV=1
O43809	Cleavage and polyadenylation specificity factor subunit 5 OS=Homo sapiens OX=9606 GN=NUDT21 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007722 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13869 all species →	NUDIX_2	Nucleotide hydrolase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000086 all species →	Domain	NUDIX hydrolase domain	Interproscan
IPR016706 all species →	Family	Cleavage/polyadenylation specificity factor subunit 5	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13047 all species →	PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005849 all species →	Cellular Component	mRNA cleavage factor complex	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:0017091 all species →	Molecular Function	mRNA 3'-UTR AU-rich region binding	Interproscan
GO:0031124 all species →	Biological Process	mRNA 3'-end processing	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
K14397	NUDT21, CPSF5, CFIM25; cleavage and polyadenylation specificity factor subunit 5	-	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_035601-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

112.1Max TPM

40.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	44.22	75.89
polyp at pH7 6	18	18	49.53	81.07
coral polyp · control treatment	16	16	39.00	78.94
coral polyp · oil and dispersant treatment	16	16	31.59	112.11
coral polyp · oil treatment	16	16	36.18	59.78
coral polyp · dispersant treatment	16	16	30.25	59.97
Polyp	10	10	60.88	110.15

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.89
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.55
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.99
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.45
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.81
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.49
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.96
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.36
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.56
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.80
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.43
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.86
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.78
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.31
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.18
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.14
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.45
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	81.07
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.35
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.74
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.43
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.93
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.98
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.50
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.70
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.78
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.21
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.27
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.58
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.08
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.92
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.42
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.13
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.06
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.94
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.69
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.33
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.62
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.07
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.92
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.06
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.38
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.93
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.78
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.39
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.77
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.19
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.64
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.20
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.11
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.23
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.62
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.34
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.25
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.42
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.36
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.37
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.04
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.52
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.95
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.06
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.19
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.46
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.07
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.46
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.78
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.61
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.35
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.83
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.87
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.27
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.99
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.40
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.97
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.82
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.46
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.80
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.32
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.52
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.97
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.65
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.86
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.48
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.16
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.85
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.80
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.84
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.41
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.39
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.90
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.82
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.02
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.68
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.17
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.06
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	110.15
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	98.34
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	69.58
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	68.96
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	65.84
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	56.03
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	43.95
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	38.08
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	31.24
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	26.61

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.