Gene detail

Detailed information of OS493_013538-T1 in Lophelia pertusa

Genomic Location: scaffold_37:821349...835314
NR annotation: KAJ7392166.1, Zinc finger CCHC domain-containing protein 7 [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
Q2KIN0	Zinc finger CCHC domain-containing protein 7 OS=Bos taurus OX=9913 GN=ZCCHC7 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005521 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00098 all species →	zf-CCHC	Zinc knuckle	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan
IPR036875 all species →	Homologous_superfamily	Zinc finger, CCHC-type superfamily	Interproscan
IPR051644 all species →	Family	TRAMP complex component and AT-rich DNA-binding protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46543 all species →	ZINC FINGER CCHC DOMAIN-CONTAINING PROTEIN 7	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0031499 all species →	Cellular Component	TRAMP complex	Interproscan
GO:0043629 all species →	Biological Process	obsolete ncRNA polyadenylation	Interproscan
GO:0071031 all species →	Biological Process	nuclear mRNA surveillance of mRNA 3'-end processing	Interproscan
GO:0071035 all species →	Biological Process	nuclear polyadenylation-dependent rRNA catabolic process	Interproscan
GO:0071036 all species →	Biological Process	nuclear polyadenylation-dependent snoRNA catabolic process	Interproscan
GO:0071037 all species →	Biological Process	nuclear polyadenylation-dependent snRNA catabolic process	Interproscan
GO:0071038 all species →	Biological Process	TRAMP-dependent tRNA surveillance pathway	Interproscan
GO:0071039 all species →	Biological Process	nuclear polyadenylation-dependent CUT catabolic process	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
K12597	AIR1_2; protein AIR1/2	-	Transfer RNA biogenesis	ko03016	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_013538-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

109TPM > 0

7Conditions

10.7Max TPM

6.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5.65	8.59
polyp at pH7 6	18	18	6.20	9.27
coral polyp · control treatment	16	16	7.77	10.70
coral polyp · oil and dispersant treatment	16	16	5.95	9.04
coral polyp · oil treatment	16	16	6.53	8.75
coral polyp · dispersant treatment	16	16	5.06	9.55
Polyp	10	9	3.80	5.81

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.59
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.96
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.59
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.40
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.18
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.93
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.91
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.43
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.04
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.97
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.87
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.87
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.37
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.32
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.09
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.27
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.15
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.10
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.02
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.01
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.73
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.57
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.56
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.37
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.31
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.20
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.01
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.54
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.93
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.23
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.18
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.70
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.50
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.07
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.58
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.58
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.53
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.05
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.46
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.22
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.14
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.10
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.04
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.91
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.61
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.04
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.16
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.57
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.38
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.75
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.64
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.45
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.20
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.16
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.07
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.82
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.76
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.23
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.03
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.85
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.16
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.75
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.58
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.35
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.73
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.64
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.31
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.28
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.95
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.91
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.70
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.56
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.47
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.04
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.04
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.25
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.93
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.55
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.47
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.80
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.74
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.19
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.06
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.12
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.04
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.95
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.16
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.78
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.94
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.01
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.51
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.78
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.81
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.71
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.79
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.61
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.87
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.98
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.90
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.34
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.