Gene detail

Detailed information of XP_066929378.1 in Clytia hemisphaerica

Genomic Location: NW_027104280.1:885687...898077
NR annotation: XP_047136407.1, ATP-citrate synthase [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

XP_066929378.1

ATGTCTTCGAAAGGAATTTATGAGGCTGATGGCAAGAAATTTTTAGCCAATCATTTGAAAGCGGACACTTTCGTCGCTCCATTGTTTGCTCATGTTGCTGAAGATACAGATTTGGAAGAATTGGCAAAAACACATCCATGGCTGTTGGAAAAGAAATTGGTGGTGAAACCGGATCAAATGATCAAACGACGTGGCAAGCTTGGTTTATTGAAAGTGAATACAAATTGGGAAGGAGTAAAAGAATGGCTGGCTGAAAAACGAGGGAAAGAAACACAGGTGGGAAAAGTGTCTGGTTTGTTGAAGAAGTTCATCATTGAACCATTCATCGAACATGACGAGAAAGAAGAGATGTATTTATGCATTTACACGCAAAGAGACGAAGACGTGATTTTGTTCCACCACGAAGGAGGTATTGACATTGGAGATGTAGATTCAAAAGCTTTGAAAATGACCATACCTATCGATGGAGAAACAAACACTGACGTCATCAAATCCACTCTCCTTTCCAATGTTGCACAAAGTGACCAAGACAGAGTGGCCCGGTTTATTTTTTCGATCTTTGACCTCTACAAAGATTTGTTTTTCACCTACCTGGAGATCAATCCTCTTGTTGTTAAGACGGACAGTATTTATGTTTTGGACCTCGCTGCAAAGATCGACCAAACGGCAGAATTTTTGTGCAGTGCCAAATGGGGCAAGATTGGTTTCCCGCCACCATTTGGACGCGAAGCCTACCCTGAAGAAGCGTTTATAGCAGAGTTGGACGCGAAGAGTGGCGCATCGTTGAAATTAACAGTGTTGAATAAAGCAGGACGTGTGTGGACCATGGTGGCCGGAGGTGGCGCCTCCGTCGTCTACAGTGACACCATCGCAGATTTGGGAGGAGGTGATGAAATGGCCAACTATGGAGAATACTCTGGCGCTCCAAGTGAAACACAGACCTTTGAATATGCAAAAACTATTTTGAAATTGATGACTGAAGGAGAACCACACCCTGATGGAAAGGTTTTAATCATCGGTGGAGGGATCGCCAACTTCACCAATGTGTCCGCTACCTTCGCCGGTATCGTGAAAGCTCTGCAACTTTACCAGCAAGAATTGATTCGCCACAAAGTGAAGATTTTCGTTCGTCGTGGAGGTCCAAATTATCAAGAAGGACTGAGGATCATGAGGGAACTTGGAGAAACATTAGGAGTACCGATGCATGTTTTTGGCACAGAAACACACATGACAGCTATCGTGGGAATGGCTCTCGGGAAAACCGAAATTCCACGTACGTCAGTGTGCGATTCGAATGATGCAGCAAGTAAAATGTTCTTCAATACATACGATGAATCAGCTCCAGCTTCAGGCAGTGGCACGCCGAAACGAAAAGCCAGCAATGAATTGACATCTAGTCAGGAGAGTGATAAAAAGAAACTTTGTAAAGCGAACAGCGGAGATTTTGTAATGGTGCAACATTCAGAAACACCTCCCTCTGTTCTCTTCACAAAAGACACAAAAGCCATCGTTTGGGGCCTTCAACACAGAGCTGTTCAGGGGATGTTGGATTTCGATTACGTGTGCCAGAGAAAGGAGCCTTCAGTCAAAGCTATGGTGTACCCTTTCAGTGGGAATCACAATCAAAAGTTTTATTATGGACACAACGAAATCATGATCCCTGTTTTCAGTAAAATGGCGGTGGCGGTTGAGAAGATTCCGGATGCTTCAGTGTTGGTGAACTTTGCTTCGTTGAGGTCAGCATACGACGCCACTGTTGATGCTCTTCAATACCCTCAGTTCCGCACAGTAGCAATCATTGCTGAAGGAATTCCCGAGAGAATCACTCAACAATTGAACAAAAAAGCCAAAGATAAAGGCGTTGTCATCATCGGTCCGGCTACCGTTGGAGGGATCAAGCCCGGTTGTTTCAAAATTGGAAACACTGGAGGAATGTTGGACAACATTCTGGCTTCCAAGTTGTACAGACCAGGAAGCATTGGTTACATTTCTCGGTCAGGAGGTTTATCCAACGAATTGAACAACATCATAGCGCGCAACACGGATGGTGTCAATGAAGGTCTGGCTATCGGTGGTGACAGATATCCCGGCACGGTATTCATCGATCATTTTCTTCGATATGAAGCCAATCCCGAGATCAAGATGATGGTCTTACTCGGAGAGGTTGGTGGTAACGACGAGTACGAAATTTGTCGCGCGATCAAAGACGGCCGCATCACGAAGCCAGTTGTCGGATGGTGTATTGGAACGTGTGCAAGTGTTTTGACGACCGAAGTCCAATTCGGACACGCCAACGCATGCGCAAACTCCTTCGCAGAAACGGCCGTCGCAAAAAATCAAGCTCTTCGAGATGCAGGAGCTGCCGTGCCCGACTCTTTTAACGACCTCGATAAAACAATCAAATCTGTTTACGAGAAGCTAGTCATGGATGGTACCATCGTCCCACGACCAGAAGTTCGCCCGCCCACCGTTCCTATGGATTACAGTTGGGCTCAGGAATTGGGATTGATTCGAAAACCTTCGTCTTTCATTTCGGCAATTTGTGACGAGAGAGGTCAAGAATTGTTGTACGCTGGTACGAAAATCTCCGACGTCTTCAAGGATGACTTGGGAATCGGAGGTGTTCTCGGCTTGTTATGGTTCCAAAGGAGATTACCGAAATATGCATCCAAATTCATTGAGATGTGTTTAATGATCACAGCTGACCATGGACCAGCGGTATCTGGCGCACATAACACCATTGTGACATCACGAGCTGGCAAAGATCTCATTTCCTCACTTTGCTCTGGTTTGCTGACAATCGGTGATCGCTTTGGTGGAGCTTTGGATGGAGCAGCCAAAATTTTCTCGGAGGCCTACGATTCAGGTACAGCGCCCATGGAGTTCGTCAATTCAATGAGAAAGAAAGGAAAGCTCATCTTGGGTATTGGCCATAAAATCAAATCGCTGAACAACCCTGACGCTCGCGTGGTGATCATGAAGAATTATATGAAAGAACATTTCCCACAGACCGACCTTTTGGATTACGCCCTGGAAGTTGAACAAATCACCACATCAAAGAAACCGAATTTGATTTTGAACGTGGATGGGTGTATTGCCGTTGGGTTTGTTGACTTGCTGAGAAACTGTGGCTGCTTTACGAGATCTGAAGCAGACGAATACGTGCAAAATGGTGCGCTCAACGGATTGTTTGTTTTAGGACGTTCTGTCGGCTTCATCGGTCACCACTTGGACCAGAAACGTCTGAAGCAAGGTTTATACAGACATCCTTGGGATGACATCTCATACATTATCCCTGAAAGTGCTCAAGCTCCTTTCGAATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P53396	ATP-citrate synthase OS=Homo sapiens OX=9606 GN=ACLY PE=1 SV=3
Q91V92	ATP-citrate synthase OS=Mus musculus OX=10090 GN=Acly PE=1 SV=1
Q2TCH3	ATP-citrate synthase OS=Ovis aries OX=9940 GN=ACLY PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005029 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02629 all species →	CoA_binding	CoA binding domain	Domain	Interproscan
PF00285 all species →	Citrate_synt	Citrate synthase, C-terminal domain	Domain	Interproscan
PF00549 all species →	Ligase_CoA	CoA-ligase	Domain	Interproscan
PF16114 all species →	Citrate_bind	ATP citrate lyase citrate-binding	Domain	Interproscan
PF08442 all species →	ATP-grasp_2	ATP-grasp domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003781 all species →	Domain	CoA-binding	Interproscan
IPR002020 all species →	Family	Citrate synthase	Interproscan
IPR014608 all species →	Family	ATP-citrate synthase	Interproscan
IPR036969 all species →	Homologous_superfamily	Citrate synthase superfamily	Interproscan
IPR005811 all species →	Domain	ATP-citrate synthase/succinyl-CoA ligase, C-terminal domain	Interproscan
IPR032263 all species →	Domain	ATP-citrate synthase, citrate-binding domain	Interproscan
IPR017866 all species →	Conserved_site	Succinyl-CoA synthetase, beta subunit, conserved site	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan
IPR016102 all species →	Homologous_superfamily	Succinyl-CoA synthetase-like	Interproscan
IPR033847 all species →	Conserved_site	ATP-citrate lyase/succinyl-CoA ligase, conserved site	Interproscan
IPR013650 all species →	Domain	ATP-grasp fold, succinyl-CoA synthetase-type	Interproscan
IPR016143 all species →	Homologous_superfamily	Citrate synthase-like, small alpha subdomain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23118 all species →	ATP-CITRATE SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046912 all species →	Molecular Function	acyltransferase activity, acyl groups converted into alkyl on transfer	Interproscan
GO:0003878 all species →	Molecular Function	ATP citrate synthase activity	Interproscan
GO:0006085 all species →	Biological Process	acetyl-CoA biosynthetic process	Interproscan
GO:0006101 all species →	Biological Process	citrate metabolic process	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006633 all species →	Biological Process	fatty acid biosynthetic process	Interproscan
GO:0003824 all species →	Molecular Function	catalytic 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
K01648	ACLY; ATP citrate (pro-S)-lyase	EC:2.3.3.8	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 XP_066929378.1 across 40 RNA-seq samples of Clytia hemisphaerica. 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.

40Samples

40TPM > 0

16Conditions

206.3Max TPM

70.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Mature medusa	5	5	58.06	64.87
medusa · Experiment Condition A1	4	4	60.16	66.76
medusa · Experiment Condition A2	4	4	58.75	61.95
medusa · Experiment Condition A3	4	4	21.34	23.63
Early gastrula	2	2	120.88	124.01
Planula 24hpf	2	2	112.92	115.91
Planula 48hpf	2	2	188.66	206.25
Planula 72hpf	2	2	128.18	150.36
Primary polyp	2	2	54.13	54.82
Gastrozooid	2	2	25.58	27.45
Gonozooid	2	2	83.70	84.09
Stolon	2	2	93.00	99.90
Baby medusa	2	2	47.71	48.88
medusa · Experiment Condition B1	2	2	36.49	40.04
medusa · Experiment Condition B2	2	2	60.53	63.71
Mixed	1	1	77.93	77.93

Per sample · hover a bar for the full sample record

Show the sample table (40 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
ERR2816251	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	64.87
ERR2816250	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	64.49
ERR2816248	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	57.39
ERR2816249	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	57.10
ERR2862245	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	46.47
ERR3299475	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	66.76
ERR3299476	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	63.69
ERR3299478	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	56.09
ERR3299477	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	54.10
ERR3299481	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	61.95
ERR3299482	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	61.01
ERR3299479	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	56.09
ERR3299480	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	55.94
ERR3299484	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	23.63
ERR3299483	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	23.15
ERR3299486	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	19.70
ERR3299485	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	18.89
ERR2816230	Early gastrula	not recorded	Early gastrula	not recorded	ERP110164	124.01
ERR2816231	Early gastrula	not recorded	Early gastrula	not recorded	ERP110164	117.75
ERR2816233	Planula 24hpf	not recorded	Planula 24hpf	not recorded	ERP110164	115.91
ERR2816232	Planula 24hpf	not recorded	Planula 24hpf	not recorded	ERP110164	109.93
ERR2816235	Planula 48hpf	not recorded	Planula 48hpf	not recorded	ERP110164	206.25
ERR2816234	Planula 48hpf	not recorded	Planula 48hpf	not recorded	ERP110164	171.06
ERR2816237	Planula 72hpf	not recorded	Planula 72hpf	not recorded	ERP110164	150.36
ERR2816236	Planula 72hpf	not recorded	Planula 72hpf	not recorded	ERP110164	105.99
ERR2816238	Primary polyp	not recorded	Primary polyp	not recorded	ERP110164	54.82
ERR2816239	Primary polyp	not recorded	Primary polyp	not recorded	ERP110164	53.44
ERR2816241	Gastrozooid	not recorded	Gastrozooid	not recorded	ERP110164	27.45
ERR2816240	Gastrozooid	not recorded	Gastrozooid	not recorded	ERP110164	23.70
ERR2816243	Gonozooid	not recorded	Gonozooid	not recorded	ERP110164	84.09
ERR2816242	Gonozooid	not recorded	Gonozooid	not recorded	ERP110164	83.31
ERR2816245	Stolon	not recorded	Stolon	not recorded	ERP110164	99.90
ERR2816244	Stolon	not recorded	Stolon	not recorded	ERP110164	86.10
ERR2816247	Baby medusa	not recorded	Baby medusa	not recorded	ERP110164	48.88
ERR2816246	Baby medusa	not recorded	Baby medusa	not recorded	ERP110164	46.54
ERR3299472	medusa · Experiment Condition B1	not recorded	medusa	Experiment Condition B1	ERP115020	40.04
ERR3299471	medusa · Experiment Condition B1	not recorded	medusa	Experiment Condition B1	ERP115020	32.93
ERR3299474	medusa · Experiment Condition B2	not recorded	medusa	Experiment Condition B2	ERP115020	63.71
ERR3299473	medusa · Experiment Condition B2	not recorded	medusa	Experiment Condition B2	ERP115020	57.35
ERR2862244	Mixed	not recorded	Mixed	not recorded	ERP110164	77.93

Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM, StringTie quantification over 40 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 Clytia hemisphaerica 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	18	XP_066919393.1	0.894959434153486
Negatively correlated	12	XP_066916465.1	-0.771268671756229

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 Clytia hemisphaerica, 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 →