Gene detail

Detailed information of OS493_023429-T1 in Lophelia pertusa

Genomic Location: scaffold_104:170696...178207
NR annotation: KAJ7384105.1, ATP-binding cassette sub- F member 2 [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
Q2KJA2	ATP-binding cassette sub-family F member 2 OS=Bos taurus OX=9913 GN=ABCF2 PE=2 SV=1
Q9UG63	ATP-binding cassette sub-family F member 2 OS=Homo sapiens OX=9606 GN=ABCF2 PE=1 SV=2
Q99LE6	ATP-binding cassette sub-family F member 2 OS=Mus musculus OX=10090 GN=Abcf2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001001 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12848 all species →	ABC_tran_Xtn	ABC transporter	Domain	Interproscan
PF00005 all species →	ABC_tran	ABC transporter	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050611 all species →	Family	ATP-binding cassette sub-family F member, EF3 subfamily	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR032781 all species →	Domain	ABC-transporter extension domain	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR017871 all species →	Conserved_site	ABC transporter-like, conserved site	Interproscan
IPR003439 all species →	Domain	ABC transporter-like, ATP-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19211 all species →	ATP-BINDING TRANSPORT PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	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
K06185	ABCF2; ATP-binding cassette, subfamily F, member 2	-	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_023429-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

145.8Max TPM

29.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.69	19.36
polyp at pH7 6	18	18	17.99	28.83
coral polyp · control treatment	16	16	23.16	57.35
coral polyp · oil and dispersant treatment	16	16	63.80	119.60
coral polyp · oil treatment	16	16	21.37	53.43
coral polyp · dispersant treatment	16	16	59.69	145.85
Polyp	10	10	9.62	18.58

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.36
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.84
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.76
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.79
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.46
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.76
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.37
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.08
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.01
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.86
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.35
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.35
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.88
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.98
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.92
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.83
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.82
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.47
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.17
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.57
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.47
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.39
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.07
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.28
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.50
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.05
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.24
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.45
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.73
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.59
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.74
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.35
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.97
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.22
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.46
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.15
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.87
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.52
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.79
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.63
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.87
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.62
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.43
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.61
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.60
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	117.57
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.08
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.83
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	77.45
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.44
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.04
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.17
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.65
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.56
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.65
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.88
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.48
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.66
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.77
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.43
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.93
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.08
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.65
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.30
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.07
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.76
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.04
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.48
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.43
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.11
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.91
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.78
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.44
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.57
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	145.85
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	105.35
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	97.06
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.62
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.06
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.98
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.72
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.05
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.87
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.85
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.67
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.72
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.38
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.56
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.30
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	18.58
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.72
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	16.66
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	14.79
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.77
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.18
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.07
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.28
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.26

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.