Gene detail

Detailed information of OS493_016316-T1 in Lophelia pertusa

Genomic Location: scaffold_50:186837...188347
NR annotation: KAJ7385247.1, leucine zipper domain binding [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
Q9CPV5	Polyamine-modulated factor 1 OS=Mus musculus OX=10090 GN=Pmf1 PE=1 SV=1
Q6P1K2	Polyamine-modulated factor 1 OS=Homo sapiens OX=9606 GN=PMF1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009094 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03980 all species →	Nnf1	Nnf1	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007128 all species →	Family	Nuclear MIS12/MIND complex subunit PMF1/Nnf1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15459 all species →	POLYAMINE-MODULATED FACTOR 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000444 all species →	Cellular Component	MIS12/MIND type complex	Interproscan
GO:0000818 all species →	Cellular Component	MIS12/MIND type complex	Interproscan
GO:0007059 all species →	Biological Process	chromosome segregation	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_016316-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_016316-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

104TPM > 0

7Conditions

26.1Max TPM

6.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	6.55	11.85
polyp at pH7 6	18	15	5.80	14.23
coral polyp · control treatment	16	16	7.26	15.41
coral polyp · oil and dispersant treatment	16	15	4.09	9.10
coral polyp · oil treatment	16	16	6.44	12.48
coral polyp · dispersant treatment	16	15	4.26	10.48
Polyp	10	9	10.85	26.11

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.85
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.23
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.18
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.76
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.18
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.83
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.29
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.51
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.08
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.16
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.04
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.96
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.57
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.36
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.97
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.22
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.90
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.23
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.24
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.47
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.82
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.58
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.92
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.54
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.20
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.89
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.78
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.73
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.70
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.39
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.64
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.28
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.41
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.60
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.07
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.94
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.86
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.33
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.28
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.09
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.48
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.83
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.36
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.81
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.76
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.43
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.10
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.64
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.20
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.78
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.13
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.48
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.16
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.40
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.64
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.02
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.86
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.19
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.48
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.67
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.48
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.92
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.13
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.85
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.18
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.96
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.90
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.82
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.41
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.53
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.42
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.80
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.48
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.84
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.10
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.07
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.77
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.59
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.13
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.74
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.99
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.67
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.61
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.29
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.28
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.87
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	26.11
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	21.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.95
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.45
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.05
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.88
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.87
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.47
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.