Gene detail

Detailed information of OS493_013628-T1 in Lophelia pertusa

Genomic Location: scaffold_37:2303997...2322389
NR annotation: KAJ7392250.1, Protein yipf3 [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
Q3B8G4	Protein YIPF3 OS=Xenopus laevis OX=8355 GN=yipf3 PE=2 SV=1
Q803Z2	Protein YIPF3 OS=Danio rerio OX=7955 GN=yipf3 PE=2 SV=1
Q9GZM5	Protein YIPF3 OS=Homo sapiens OX=9606 GN=YIPF3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006219 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for OS493_013628-T1 in Lophelia pertusa.

InterPro

InterPro term	Type	Description	Source
IPR051521 all species →	Family	tRNA Modification and Golgi Maintenance Protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15627 all species →	NATURAL KILLER CELL-SPECIFIC ANTIGEN KLIP1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005794 all species →	Cellular Component	Golgi apparatus	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
K22941	YIPF3, KLIP1; protein YIPF3	-	Membrane trafficking	ko04131	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_013628-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

39.2Max TPM

19.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.39	19.49
polyp at pH7 6	18	18	14.33	18.35
coral polyp · control treatment	16	16	25.08	39.18
coral polyp · oil and dispersant treatment	16	16	25.56	34.37
coral polyp · oil treatment	16	16	22.49	31.55
coral polyp · dispersant treatment	16	16	21.41	30.18
Polyp	10	9	9.38	17.71

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.49
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.21
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.45
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.26
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.93
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.46
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.30
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.14
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.01
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.28
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.02
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.75
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.69
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.64
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.08
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.87
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.82
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.68
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.35
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.23
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.07
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.05
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.62
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.90
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.39
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.29
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.08
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.84
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.47
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.61
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.30
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.29
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.60
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.58
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.77
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.56
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.18
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.72
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.81
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.90
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.68
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.17
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.27
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.03
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.50
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.86
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.41
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.24
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.32
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.28
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.66
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.26
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.37
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.84
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.28
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.18
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.67
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.32
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.09
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.98
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.83
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.38
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.60
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.59
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.91
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.71
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.27
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.46
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.96
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.73
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.22
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.34
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.21
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.90
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.42
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.77
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.22
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.15
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.68
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.87
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.18
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.13
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.03
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.12
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.73
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.53
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.97
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.59
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.65
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.89
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.28
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.64
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.08
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.00
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.71
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.71
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.55
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.16
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.67
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.12
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.14
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.70
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.10
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.