Gene detail

Detailed information of OS493_002107-T1 in Lophelia pertusa

Genomic Location: scaffold_4:5268887...5272178
NR annotation: KAJ7375356.1, Cytoplasmic dynein 1 intermediate chain 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
Q0III3	Cytoplasmic dynein 1 intermediate chain 2 OS=Bos taurus OX=9913 GN=DYNC1I2 PE=1 SV=1
Q13409	Cytoplasmic dynein 1 intermediate chain 2 OS=Homo sapiens OX=9606 GN=DYNC1I2 PE=1 SV=3
Q5NVM2	Cytoplasmic dynein 1 intermediate chain 2 OS=Pongo abelii OX=9601 GN=DYNC1I2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006423 (this species only)
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR050687 all species →	Family	Dynein Intermediate Chain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12442 all species →	DYNEIN INTERMEDIATE CHAIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005868 all species →	Cellular Component	cytoplasmic dynein complex	Interproscan
GO:0007018 all species →	Biological Process	microtubule-based movement	Interproscan
GO:0010970 all species →	Biological Process	transport along microtubule	Interproscan
GO:0045503 all species →	Molecular Function	dynein light chain binding	Interproscan
GO:0045504 all species →	Molecular Function	dynein heavy chain 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_002107-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_002107-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

53.0Max TPM

27.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	21.80	26.55
polyp at pH7 6	18	18	22.01	27.87
coral polyp · control treatment	16	16	35.26	49.87
coral polyp · oil and dispersant treatment	16	16	28.14	42.25
coral polyp · oil treatment	16	16	34.83	52.98
coral polyp · dispersant treatment	16	16	28.87	46.59
Polyp	10	10	25.01	36.99

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.55
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.54
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.87
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.30
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.24
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.71
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.55
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.52
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.47
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.76
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.43
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.54
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.45
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.42
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.41
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.18
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.46
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.03
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.87
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.97
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.87
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.43
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.08
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.09
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.88
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.45
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.95
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.73
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.15
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.01
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.89
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.84
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.72
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.04
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.15
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.87
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.19
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.36
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.17
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.66
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.65
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.68
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.28
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.09
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.34
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.55
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.99
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.36
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.42
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.18
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.03
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.98
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.72
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.34
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.85
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.56
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.67
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.02
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.14
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.46
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.04
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.77
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.59
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.75
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.98
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.82
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.87
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.20
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.32
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.77
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.91
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.23
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.41
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.80
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.57
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.38
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.23
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.38
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.71
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.59
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.14
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.93
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.92
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.28
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.27
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.71
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.22
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.25
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.09
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.66
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.29
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.78
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.24
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.10
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	36.99
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	34.80
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	31.75
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	27.14
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	26.28
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	25.72
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	23.38
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.23
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.72
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	13.07

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.