Gene detail

Detailed information of OS493_015591-T1 in Lophelia pertusa

Genomic Location: scaffold_47:729501...732976
NR annotation: KAJ7360490.1, Tubulin beta-4A chain [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
Q3MHM5	Tubulin beta-4B chain OS=Bos taurus OX=9913 GN=TUBB4B PE=1 SV=1
P68371	Tubulin beta-4B chain OS=Homo sapiens OX=9606 GN=TUBB4B PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000512 (this species only)

Pfam domain

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

InterPro

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

PANTHER

PANTHER term	Description	Source
PTHR11588 all species →	TUBULIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005874 all species →	Cellular Component	microtubule	Interproscan
GO:0007017 all species →	Biological Process	microtubule-based process	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005200 all species →	Molecular Function	structural constituent of cytoskeleton	Interproscan
GO:0000226 all species →	Biological Process	microtubule cytoskeleton organization	Interproscan
GO:0000278 all species →	Biological Process	mitotic cell cycle	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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_015591-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

92.3Max TPM

33.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	77.06	91.38
polyp at pH7 6	18	18	74.50	92.28
coral polyp · control treatment	16	16	8.63	14.56
coral polyp · oil and dispersant treatment	16	16	6.06	8.63
coral polyp · oil treatment	16	16	7.19	18.40
coral polyp · dispersant treatment	16	16	7.71	19.28
Polyp	10	10	53.21	76.57

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	91.38
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	90.36
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	88.45
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	85.22
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	84.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	83.05
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	81.57
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.72
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.41
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	74.87
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	74.47
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	73.51
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	73.49
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.65
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.82
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.17
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.62
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.61
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.28
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	89.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	81.56
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	81.56
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.56
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.28
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	79.95
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	77.64
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.46
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.37
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.15
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.07
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.33
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.27
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.58
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.01
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.52
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.15
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.56
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.65
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.30
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.91
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.10
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.02
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.22
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.50
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.89
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.82
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.71
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.62
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.33
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.73
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.90
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.63
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.53
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.71
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.06
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.79
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.78
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.56
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.76
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.73
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.69
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.63
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.36
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.32
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.31
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.70
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.40
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.37
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.93
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.62
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.35
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.22
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.04
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.78
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.67
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.06
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.88
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.77
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.39
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.91
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.55
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.28
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.88
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.18
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.86
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.01
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.79
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.19
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.02
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.64
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.92
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.56
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.56
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.53
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.43
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.74
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.72
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	76.57
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	70.82
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	68.34
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	61.13
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	59.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	55.36
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	47.94
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	33.42
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	32.01
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	27.45

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.