Gene detail

Detailed information of OS493_028019-T1 in Lophelia pertusa

Genomic Location: scaffold_157:228581...237185
NR annotation: KAJ7389967.1, hypothetical protein OS493_028019 [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
P11833	Tubulin beta chain OS=Paracentrotus lividus OX=7656 PE=2 SV=1
P30883	Tubulin beta-4 chain OS=Xenopus laevis OX=8355 GN=tubb4 PE=1 SV=1
Q3MHM5	Tubulin beta-4B chain OS=Bos taurus OX=9913 GN=TUBB4B PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000525 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00091 all species →	Tubulin	Tubulin/FtsZ family, GTPase domain	Domain	Interproscan
PF03953 all species →	Tubulin_C	Tubulin C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017975 all species →	Conserved_site	Tubulin, conserved site	Interproscan
IPR018316 all species →	Domain	Tubulin/FtsZ, 2-layer sandwich domain	Interproscan
IPR003008 all species →	Domain	Tubulin/FtsZ, GTPase domain	Interproscan
IPR000217 all species →	Family	Tubulin	Interproscan
IPR036525 all species →	Homologous_superfamily	Tubulin/FtsZ, GTPase domain superfamily	Interproscan
IPR002453 all species →	Family	Beta tubulin	Interproscan
IPR013838 all species →	Binding_site	Beta tubulin, autoregulation binding site	Interproscan
IPR008280 all species →	Homologous_superfamily	Tubulin/FtsZ, C-terminal	Interproscan
IPR037103 all species →	Homologous_superfamily	Tubulin/FtsZ-like, C-terminal domain	Interproscan
IPR023123 all species →	Homologous_superfamily	Tubulin, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11588 all species →	TUBULIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0005874 all species →	Cellular Component	microtubule	Interproscan
GO:0007017 all species →	Biological Process	microtubule-based process	Interproscan
GO:0000226 all species →	Biological Process	microtubule cytoskeleton organization	Interproscan
GO:0000278 all species →	Biological Process	mitotic cell cycle	Interproscan
GO:0005200 all species →	Molecular Function	structural constituent of cytoskeleton	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	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
K07375	TUBB; tubulin beta	-	Exosome	ko04147	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_028019-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

108TPM > 0

7Conditions

15.7Max TPM

4.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	4.61	10.35
polyp at pH7 6	18	18	5.62	15.66
coral polyp · control treatment	16	16	4.14	7.61
coral polyp · oil and dispersant treatment	16	15	2.81	5.55
coral polyp · oil treatment	16	16	2.40	4.65
coral polyp · dispersant treatment	16	16	5.31	7.56
Polyp	10	10	7.42	14.02

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.35
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.93
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.90
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.46
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.40
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.14
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.04
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.95
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.88
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.86
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.67
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.67
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.29
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.08
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.18
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.09
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.06
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.66
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.78
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.97
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.61
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.88
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.97
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.94
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.71
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.67
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.37
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.34
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.91
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.51
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.07
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.85
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.31
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.61
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.48
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.27
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.09
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.74
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.20
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.16
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.93
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.43
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.29
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.11
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.80
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.73
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.63
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.55
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.15
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.11
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.00
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.63
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.46
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.88
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.30
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.26
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.89
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.67
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.86
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.65
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.27
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.02
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.24
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.87
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.56
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.30
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.07
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.79
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.63
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.57
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.23
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.19
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.15
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.95
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.56
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.44
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.91
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.79
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.76
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.51
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.18
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.87
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.07
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.16
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.89
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.10
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.28
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.90
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.24
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.99
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.89
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.09
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.85
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.49

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.