Gene detail

Detailed information of OS493_011907-T1 in Lophelia pertusa

Genomic Location: scaffold_30:3022883...3028195
NR annotation: KAJ7336685.1, regulation of translation [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
Q3ZC67	Polyadenylate-binding protein-interacting protein 2 OS=Bos taurus OX=9913 GN=PAIP2 PE=2 SV=1
Q9D6V8	Polyadenylate-binding protein-interacting protein 2 OS=Mus musculus OX=10090 GN=Paip2 PE=1 SV=1
Q6AXZ0	Polyadenylate-binding protein-interacting protein 2 OS=Rattus norvegicus OX=10116 GN=Paip2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009031 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07145 all species →	PAM2	Ataxin-2 C-terminal region	Motif	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009818 all species →	Domain	Ataxin-2, C-terminal	Interproscan
IPR040396 all species →	Family	Polyadenylate-binding protein-interacting protein 2-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13154 all species →	POLYADENYLATE-BINDING PROTEIN-INTERACTING PROTEIN 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000900 all species →	Molecular Function	mRNA regulatory element binding translation repressor activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0017148 all species →	Biological Process	negative regulation of translation	Interproscan
GO:0030371 all species →	Molecular Function	translation repressor activity	Interproscan
GO:0045947 all species →	Biological Process	negative regulation of translational initiation	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
K27470	PAIP2; polyadenylate-binding protein-interacting protein 2	-	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_011907-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

297.8Max TPM

158.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	155.25	178.96
polyp at pH7 6	18	18	167.79	261.03
coral polyp · control treatment	16	16	157.61	252.20
coral polyp · oil and dispersant treatment	16	16	153.16	220.66
coral polyp · oil treatment	16	16	140.08	221.41
coral polyp · dispersant treatment	16	16	157.10	297.81
Polyp	10	10	192.47	239.30

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	-	178.96
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	173.01
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	169.09
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	167.56
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	166.16
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	165.85
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	165.08
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	164.38
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	161.18
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	155.30
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	154.19
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	152.91
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	148.11
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	142.74
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	141.67
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	139.69
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	127.51
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	121.11
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	261.03
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	227.15
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	187.65
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	186.78
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	182.85
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	177.73
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	167.95
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	162.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	160.63
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	151.72
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	148.69
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	147.85
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	147.71
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	147.17
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	142.70
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	140.95
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	140.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	139.50
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	252.20
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	208.50
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	176.27
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	176.23
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	171.18
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	169.47
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	167.61
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	154.29
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	146.70
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	144.23
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	133.83
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	133.55
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	131.55
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	130.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	128.55
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.53
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	220.66
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	191.17
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	179.79
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	173.76
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	166.27
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	162.21
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	161.74
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	160.37
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	154.30
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	139.38
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	135.38
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	132.77
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	125.59
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	121.88
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	114.20
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.06
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	221.41
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	164.40
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	157.92
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	157.88
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	153.19
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	148.18
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	142.60
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	140.07
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	139.60
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	136.46
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	128.42
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	126.50
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.44
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	109.33
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	102.31
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	100.53
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	297.81
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	276.29
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	176.20
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	175.28
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	173.65
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	166.78
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	149.53
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	141.23
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	135.54
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	132.34
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	123.34
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	121.36
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	115.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	112.71
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	111.08
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	105.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	239.30
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	234.63
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	234.57
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	218.65
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	201.48
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	177.96
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	175.79
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	149.22
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	146.66
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	146.46

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.