Gene detail

Detailed information of HSymV2.0_g01.00214_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_1:6322361...6330561
NR annotation: XP_002163780.1, ATP synthase subunit alpha, mitochondrial [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · 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
P19483	ATP synthase F(1) complex subunit alpha, mitochondrial OS=Bos taurus OX=9913 GN=ATP5F1A PE=1 SV=1
P80021	ATP synthase F(1) complex subunit alpha, mitochondrial OS=Sus scrofa OX=9823 GN=ATP5F1A PE=1 SV=2
Q5R546	ATP synthase F(1) complex subunit alpha, mitochondrial OS=Pongo abelii OX=9601 GN=ATP5F1A PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003945 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00306 all species →	ATP-synt_ab_C	ATP synthase alpha/beta chain, C terminal domain	Domain	Interproscan
PF00006 all species →	ATP-synt_ab	ATP synthase alpha/beta family, nucleotide-binding domain	Domain	Interproscan
PF02874 all species →	ATP-synt_ab_N	ATP synthase alpha/beta family, beta-barrel domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005294 all species →	Family	ATP synthase, F1 complex, alpha subunit	Interproscan
IPR036121 all species →	Homologous_superfamily	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily	Interproscan
IPR000793 all species →	Domain	ATP synthase, alpha subunit, C-terminal	Interproscan
IPR033732 all species →	Domain	ATP synthase, F1 complex, alpha subunit nucleotide-binding domain	Interproscan
IPR000194 all species →	Domain	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR004100 all species →	Domain	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Interproscan
IPR020003 all species →	Active_site	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Interproscan
IPR038376 all species →	Homologous_superfamily	ATP synthase, alpha subunit, C-terminal domain superfamily	Interproscan
IPR023366 all species →	Homologous_superfamily	ATP synthase subunit alpha, N-terminal domain-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48082 all species →	ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015986 all species →	Biological Process	proton motive force-driven ATP synthesis	Interproscan
GO:0045261 all species →	Cellular Component	proton-transporting ATP synthase complex, catalytic core F(1)	Interproscan
GO:0046933 all species →	Molecular Function	proton-transporting ATP synthase activity, rotational mechanism	Interproscan
GO:0046034 all species →	Biological Process	ATP metabolic process	Interproscan
GO:1902600 all species →	Biological Process	proton transmembrane transport	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005754 all species →	Cellular Component	obsolete mitochondrial proton-transporting ATP synthase, catalytic core	Interproscan
GO:0043531 all species →	Molecular Function	ADP binding	Interproscan
GO:0032559 all species →	Molecular Function	adenyl ribonucleotide binding	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
K02132	ATPeF1A, ATP5A1, ATP1; F-type H+-transporting ATPase subunit alpha	-	Diabetic cardiomyopathy	ko05415	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of HSymV2.0_g01.00214_t1 across 44 RNA-seq samples of Hydractinia symbiolongicarpus. 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.

44Samples

44TPM > 0

3Conditions

770.3Max TPM

540.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	519.35	770.35
Whole embryo · Triptolide 20 uM	4	4	599.68	646.01
Whole embryo · DMSO 0.5%	4	4	668.53	719.47

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	770.35
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	740.58
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	697.95
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	685.95
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	661.53
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	648.20
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	622.53
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	606.89
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	605.31
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	582.59
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	582.21
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	563.37
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	553.97
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	553.34
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	535.07
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	533.56
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	526.48
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	513.30
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	509.12
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	502.93
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	470.24
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	464.88
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	453.07
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	449.98
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	449.72
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	440.61
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	440.36
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	427.68
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	417.90
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	412.25
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	399.39
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	391.92
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	384.58
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	380.40
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	369.88
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	348.59
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	646.01
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	635.87
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	576.49
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	540.36
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	719.47
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	704.84
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	650.06
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	599.75

Source: CnidoSite RNA-seq expression matrices (HSYMB_TPM, StringTie quantification over 44 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 Hydractinia symbiolongicarpus 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	9	HSymV2.0_g05.08422_t1	0.866866801616342
Negatively correlated	31	HSymV2.0_g04.07545_t1	-0.815741280946568

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.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Hydractinia symbiolongicarpus, 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 →