Gene detail

Detailed information of ENSBQFP00000020377.1 in Heliopora coerulea

Genomic Location: JASJOG010000036.1:206505...229703
NR annotation: XP_046846747.1, tubulin gamma-1 chain [Xenia sp. Carnegie-2017]
Species Heliopora coerulea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q0VCD2	Tubulin gamma-1 chain OS=Bos taurus OX=9913 GN=TUBG1 PE=2 SV=1
P23258	Tubulin gamma-1 chain OS=Homo sapiens OX=9606 GN=TUBG1 PE=1 SV=2
P23330	Tubulin gamma-1 chain OS=Xenopus laevis OX=8355 GN=tubg1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007083 (this species only) · gene tree & orthology

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
IPR036525 all species →	Homologous_superfamily	Tubulin/FtsZ, GTPase domain superfamily	Interproscan
IPR000217 all species →	Family	Tubulin	Interproscan
IPR037103 all species →	Homologous_superfamily	Tubulin/FtsZ-like, C-terminal domain	Interproscan
IPR018316 all species →	Domain	Tubulin/FtsZ, 2-layer sandwich domain	Interproscan
IPR008280 all species →	Homologous_superfamily	Tubulin/FtsZ, C-terminal	Interproscan
IPR003008 all species →	Domain	Tubulin/FtsZ, GTPase domain	Interproscan
IPR017975 all species →	Conserved_site	Tubulin, conserved site	Interproscan
IPR002454 all species →	Family	Gamma tubulin	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: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:0000070 all species →	Biological Process	mitotic sister chromatid segregation	Interproscan
GO:0000212 all species →	Biological Process	meiotic spindle organization	Interproscan
GO:0000226 all species →	Biological Process	microtubule cytoskeleton organization	Interproscan
GO:0000278 all species →	Biological Process	mitotic cell cycle	Interproscan
GO:0000930 all species →	Cellular Component	gamma-tubulin complex	Interproscan
GO:0005200 all species →	Molecular Function	structural constituent of cytoskeleton	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005813 all species →	Cellular Component	centrosome	Interproscan
GO:0005819 all species →	Cellular Component	spindle	Interproscan
GO:0007020 all species →	Biological Process	microtubule nucleation	Interproscan
GO:0007052 all species →	Biological Process	mitotic spindle organization	Interproscan
GO:0031122 all species →	Biological Process	cytoplasmic microtubule organization	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
K10389	TUBG; tubulin gamma	-	Cytoskeleton proteins	ko04812	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000020377.1 across 37 RNA-seq samples of Heliopora coerulea. 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.

37Samples

35TPM > 0

6Conditions

164.0Max TPM

57.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	17	67.41	103.39
polyp and skeleton · 31C, 3week	6	6	50.75	67.43
polyp and skeleton · 28C, 3week	6	5	57.37	164.03
polyp and skeleton · 26C, 3week	4	4	50.09	73.86
polyp and skeleton · 28C, 24hr	2	2	40.24	41.54
polyp and skeleton · 31C, 24hr	2	1	31.38	62.77

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	103.39
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	95.47
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	81.02
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	78.62
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	76.81
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	72.78
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	72.20
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	70.94
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	65.30
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	62.75
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	61.11
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	57.18
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	56.66
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	53.89
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	49.97
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	47.89
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	39.99
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	67.43
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	52.80
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	52.37
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	44.88
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	44.76
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	42.29
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	164.03
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	48.94
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	46.57
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	43.13
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	41.52
SRR12578067	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	0.00
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	73.86
SRR12587801	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	64.42
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	32.11
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	29.96
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	41.54
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	38.95
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	62.77
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	0.00

Source: CnidoSite RNA-seq expression matrices (HCOER_TPM, StringTie quantification over 37 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.

Co-expression network

Genes whose expression across the transcriptome samples of Heliopora coerulea tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	25	ENSBQFP00000018754	0.877113711929725
Negatively correlated	10	ENSBQFP00000038316	-0.711725428407008

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list. Partner counts were matched on ENSBQFP00000020377, the spelling this network uses.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Heliopora coerulea, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →