Gene detail

Detailed information of OS493_029823-T1 in Lophelia pertusa

Genomic Location: scaffold_185:185369...194758
NR annotation: KAJ7354817.1, Intraflagellar transport protein 43 [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
B5XBI1	Intraflagellar transport protein 43 homolog A OS=Salmo salar OX=8030 GN=ift43a PE=2 SV=1
Q9DA69	Intraflagellar transport protein 43 homolog OS=Mus musculus OX=10090 GN=Ift43 PE=1 SV=2
B5X7E4	Intraflagellar transport protein 43 homolog B OS=Salmo salar OX=8030 GN=ift43b PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003689 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF15305 all species →	IFT43	Intraflagellar transport protein 43	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029302 all species →	Family	Intraflagellar transport protein 43	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR33724 all species →	INTRAFLAGELLAR TRANSPORT PROTEIN 43 HOMOLOG	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005929 all species →	Cellular Component	cilium	Interproscan
GO:0030991 all species →	Cellular Component	intraciliary transport particle A	Interproscan
GO:0035721 all species →	Biological Process	intraciliary retrograde transport	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
K19675	IFT43; intraflagellar transport protein 43	-	Cilium and associated proteins	ko03037	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_029823-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

59.2Max TPM

28.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	34.05	49.66
polyp at pH7 6	18	18	32.85	43.69
coral polyp · control treatment	16	16	30.14	55.25
coral polyp · oil and dispersant treatment	16	16	25.00	59.16
coral polyp · oil treatment	16	16	29.32	36.35
coral polyp · dispersant treatment	16	16	20.49	34.40
Polyp	10	10	28.59	49.45

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.66
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.83
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.83
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.04
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.43
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.78
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.24
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.55
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.19
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.71
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.26
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.67
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.04
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.86
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.85
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.69
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.69
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.59
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.18
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.45
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.45
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.36
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.98
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.41
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.29
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.74
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.94
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.40
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.66
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.03
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.58
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.24
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.25
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.56
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.71
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.17
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.71
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.08
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.80
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.62
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.34
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.12
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.92
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.92
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.07
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.28
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.16
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.35
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.45
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.69
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.17
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.05
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.03
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.32
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.22
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.81
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.20
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.06
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.70
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.81
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.35
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.86
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.48
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.62
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.07
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.37
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.24
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.43
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.39
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.28
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.10
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.55
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.54
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.82
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.59
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.40
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.30
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.64
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.52
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.43
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.32
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.79
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.70
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.46
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.11
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.70
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.39
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.44
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.06
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.32
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.32
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	49.45
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	46.60
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	46.58
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	31.40
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	23.69
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	21.67
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	20.72
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.48
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	15.42
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.88

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.