Gene detail

Detailed information of OS493_000795-T1 in Lophelia pertusa

Genomic Location: scaffold_2:297768...298537
NR annotation: KAJ7387466.1, cell differentiation [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
Q8HZ57	Coiled-coil alpha-helical rod protein 1 OS=Pan paniscus OX=9597 GN=CCHCR1 PE=3 SV=1
Q8HZ60	Coiled-coil alpha-helical rod protein 1 OS=Pan troglodytes OX=9598 GN=CCHCR1 PE=3 SV=1
Q8HZ58	Coiled-coil alpha-helical rod protein 1 OS=Pongo pygmaeus OX=9600 GN=CCHCR1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007464 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07111 all species →	HCR	Alpha helical coiled-coil rod protein (HCR)	Coiled-coil	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009800 all species →	Family	Coiled-coil alpha-helical rod protein 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46822 all species →	COILED-COIL ALPHA-HELICAL ROD PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005814 all species →	Cellular Component	centriole	Interproscan
GO:0006611 all species →	Biological Process	protein export from nucleus	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	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_000795-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_000795-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

93TPM > 0

7Conditions

13.6Max TPM

2.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	3.20	6.18
polyp at pH7 6	18	11	2.39	9.28
coral polyp · control treatment	16	16	3.27	13.58
coral polyp · oil and dispersant treatment	16	15	1.66	2.86
coral polyp · oil treatment	16	15	2.87	7.01
coral polyp · dispersant treatment	16	13	1.07	3.57
Polyp	10	7	1.66	3.41

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	-	6.18
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.19
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.48
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.39
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.30
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.30
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.68
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.64
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.45
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.34
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.97
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.69
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.44
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.34
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.17
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.02
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.28
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.82
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.68
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.53
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.58
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.23
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.60
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.58
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.98
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.81
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.58
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.75
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.61
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.19
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.76
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.74
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.68
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.56
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.76
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.73
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.64
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.45
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.30
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.91
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.82
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.84
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.46
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.29
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.02
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.68
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.55
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.41
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.19
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.16
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.01
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.88
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.50
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.22
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.04
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.97
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.84
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.44
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.62
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.60
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.60
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.66
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.57
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.57
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.36
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.09
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.45
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.19
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.86
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.37
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.24
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.41
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.77
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.44
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.19
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.06
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.93
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.77
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
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.