Gene detail

Detailed information of OS493_004414-T1 in Lophelia pertusa

Genomic Location: scaffold_8:6294751...6301526
NR annotation: KAJ7387419.1, hypothetical protein OS493_004414 [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
P17630	Transcobalamin-1 OS=Sus scrofa OX=9823 GN=TCN1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001572 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01122 all species →	Cobalamin_bind	Eukaryotic cobalamin-binding protein	Repeat	Interproscan
PF14478 all species →	DUF4430	Domain of unknown function (DUF4430)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008930 all species →	Homologous_superfamily	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Interproscan
IPR051588 all species →	Family	Eukaryotic Cobalamin Transport	Interproscan
IPR002157 all species →	Family	Cobalamin (vitamin B12)-binding protein	Interproscan
IPR027954 all species →	Domain	Transcobalamin-like, C-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10559 all species →	TRANSCOBALAMIN-1/GASTRIC INTRINSIC FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015889 all species →	Biological Process	cobalamin transport	Interproscan
GO:0031419 all species →	Molecular Function	cobalamin binding	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_004414-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_004414-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

48.1Max TPM

17.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.16	25.29
polyp at pH7 6	18	18	14.20	19.51
coral polyp · control treatment	16	16	23.38	48.07
coral polyp · oil and dispersant treatment	16	16	21.43	38.28
coral polyp · oil treatment	16	16	19.03	28.64
coral polyp · dispersant treatment	16	16	21.79	46.29
Polyp	10	10	6.94	25.60

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.29
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.08
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.27
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.41
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.04
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.70
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.05
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.40
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.81
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.58
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.57
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.18
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.38
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.99
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.82
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.58
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.31
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.51
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.63
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.45
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.34
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.02
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.59
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.10
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.23
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.54
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.19
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.03
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.90
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.74
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.81
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.07
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.61
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.73
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.66
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.14
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.96
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.04
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.74
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.04
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.78
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.70
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.42
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.03
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.35
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.28
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.48
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.76
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.75
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.62
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.14
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.04
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.82
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.04
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.73
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.05
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.91
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.80
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.79
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.45
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.16
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.64
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.36
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.12
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.26
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.76
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.55
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.65
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.91
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.75
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.14
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.42
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.33
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.13
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.03
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.97
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.51
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.29
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.56
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.40
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.70
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.65
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.96
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.53
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.20
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.55
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.81
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.29
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.76
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.97
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.82
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	25.60
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.72
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.87
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.44
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.41
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.72
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.34
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.90
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.36

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.