Gene detail

Detailed information of XP_066910854.1 in Clytia hemisphaerica

Genomic Location: NW_027103443.1:16104...38707
NR annotation: XP_047134564.1, valine--tRNA ligase isoform X2 [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

XP_066910854.1

ATGAGGCAAATGGTAGTCACTTTCGCTCTTCTGAGAAATTGCATCAGACAAGTCAATTCTTCACAATTTTTCATCAGCTCAATACGATCTAAGCATCAATTTTGTTTAAATGGTAGTCTAGGGGTACCTAGACGTCAAATATCATCGAGTTACTTAATACTTACAAAGAAAATGAGTTCAACTGAAGGGGAAAATCGGCCTCCTGCAGAAAATGATTGCGAAGAAGTTGTCAAGACAGCTAGCCAGCTGAAAAAAGAAGCAAAACGACTTGCAAAAATGGAAAAATTTGCCAAGAAACAAGAGCAGTCAAAGCAGAATAAACCTAAAGAGGAGAAACCTAAAGCAAAGAAGGAAAAAGTTACAACCAAGCAGGTCATCACTTATGATATCCAAACACCCGCTGGTGACAAAAAAGATACAAAATGTACACTACCTGATGCATACAGTCCATCTTATGTTGAAAGCGCTTGGTATTCTTGGTGGGAGAAAAAGGGATTTTTCAAACCAGAATATGGGAGAGAATCAATCACTGAAAAAAATGATAAAGGAAATTTCACTATTGTTATCCCACCTCCAAATGTCACAGGAAATCTTCATTTAGGACATGCCTTGACTGGGGCTATTGAAGATGCTGTTACTAGATGGCATCGTATGAATGGAAAAACCACTCTTTATCTTCCTGGTTGTGACCATGCTGGCATTGCAACTCAAGTTGTTGTTGAAAGACAGTTGAAGAAAGAACAAAATCTTAGCCGTCATGATCTTGGCCGTGAAAAGTTTGTTGAAAAAGTGTGGGAATGGAAAAACAAGAAAGGAGATCGTATTTATCATCAAATTCGAAAACTTGGTAGTTCCGTTGATTGGGAAAGAGCCTCGTTTACTATGGATGAAAAGTTATCAAAGGCTGTCAAAGAAACGTTTATTAGATTGCATGATGAGAAACTGATTTATCGATCAAACCGTCTTGTCAACTGGTCTTGTGCTTTGAATTCTGCAATTAGTGATATTGAGGTTGACAAAAAGGATATTGGAGGAAGAACCTTACTCAGTGTACCTGGCTATGAACAGAAAATTGAATTTGGTGTTCTCATCCACTTCACCTATCCTGTTGAGGGATCAGATGAGAAGTTAACGGTAGCTACAACACGTATTGAAACTATGGTTGGTGATACTGGAATTGCTGTCCACCCCACTGATGAAAGATATAAACATTTGGTTGGTAAACATGCATTGCATCCGTTTTGTAATAGAAAACTGTTGATTGTCGGTGATGAAGCAGTCGATCCAGAATTTGGAACTGGTGCTGTCAAGATTACACCAGGTCATGATCACAATGATTATGAAATCGGAAAGCGACATAATTTACGCTTCATCACCATGATGGATGATGCTGGTCTGTGCACTGATGTCGGTGATTACAAAGATGAATACAAGAAATTCATTAAAATGAAACGTTTCGTAGCCAGATATGAAGTTTTGAATGAATTGAAAGCCATTGGTTCCTACGTCAAGACCGAAGATAATGCTATGGTTGTCCCAACTTGCAGTCGCTCAAAAGATATTGTCGAACCGTTATTGAAGCCACAGTGGTATGTCGATTGCAAAGAGATGGCTGCCAAAGCTGTTTCGGCTGTTCGTGATGGAGATCTCAAAATTATTCCAAGTATGCACGAAAAAACGTGGTATCAATGGATGGAGAACTCGAGAGATTGGTGTATTTCACGTCAATTATGGTGGGGTCATCGTATACCGGCTTACTACGTCACCATTTTGGGTGAACCATCCGGCTCGGACGAAGAAGAAAAGTATTGGGTCAGCGGGCGCTCGGAAGACGAAGCTCTTGAGAAAGCAGCTAAACAGTTCAATGTTCCAAAAGAAAAGATTCACTTGAGACAAGATGAGGATGTTTTGGACACGTGGTTCTCCTCAGCCCTTTTTCCTTTCTCCGTCTTCGGATGGCCTGATAACACGGACGAGATGGAAGCATTCTACCCAACCTCCCTTTTGGAGACTGGACACGATATTTTATTTTTCTGGGTCGCTCGTATGGTCATGTTTGGACAGAAATTGACTGGAAGACTACCATTTAAAGAGGTTTATCTTCACGCCATGGTGAGAGATGCATACGGACGGAAGATGAGCAAATCTCTTGGAAACATCATCGACCCATTGGATGTCATCACTGGTATCTCACTACCAGACTTGATGGGAAGATTGAACGAATATAATCTGGACCCAAAAGAATTGGAGAAAGCGCAGAAGGGACAGAAGGAGATGTACCCAGACGGTATTCCAGAATGTGGCACTGATGCTATGCGATTCGCTTTGTGTGCTTACACACTTCAAGGACGTGATATCAACTTGGACGTTTTAAGAATGCAAGGATATCGACATTTCTGTAACAAGCTTTGGAACGCTACCAAATTCGCCATGAGGAATTTCACACCAGAATTTCTCCCAAGAAGTAACTTGAAAGAGCTTTCCGGACAAGAAACTGCAATGGACTTGTGGATTTTGAGTCGCCTATCGGTAGCTGCAACTCTCTGCAACGAAGGATTCCAATCGTACGAATTCCCGAAAGCAACGACCGCTTTGTACAACTTCTGGCTCTACGAATTATGTGATGTTTATTTGGAATCGTTGAAGCCAATCTTCCAAGGTGACGACGAAAAGCAAAAGATTTGTGCACAAAATGTTCTATACACGTGTCTTGATGCGGGGTTACGTATGTTGAGTCCGTTCATGCCGTACGTTACGGAAGAATTGTATCAACGTTTACCGCACAACAAAGAAACAGTCCCTGAAAGCATTTGTGTCGCTTCGTATCCTAAAGATTGGAATTTACGAAATGAGGCAATCGAAAAGCAGATCGAACACATGATGGAAATCGTCAAGACCATTCGCTCCAAGAAGGATGAATACATGAGCAACAAATCTAAGTGCTTAGTTTACGTTCGTCCGCACCAAAATTATTCTAAAGAAGTTGTTGAAAAGCTGAATGACGTCATCAAAACACTGTCTCAATCGTCTGAAATTCAACTACTTGGTGAAAAGGAGGAAGCACCCGGAGGTTGCGCTATCCAACTTGTTGGTGATAAATGTGAAGTCTTACTCTCACTCAAGGGTATTGTCGACTTCACTAAAGAAATCCAAAAGCTTCGAGTCAAACAAGAAAAGTCTGAACAATCCGTTAGCAAACTTATCGAAACCACGAAGAAAGACGACTATGAAACCAAGGTTCCAGAAAAAGTTCGAGAACAGAATCAACAAAAGATTACACAACTTCACACCGAGATTGAAAAGTTGAAAATCACAATCGATACATTCGAGCAAGCTGCGAAAGATGCCTCGTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P49696	Valine--tRNA ligase OS=Takifugu rubripes OX=31033 GN=vars1 PE=3 SV=1
Q9Z1Q9	Valine--tRNA ligase OS=Mus musculus OX=10090 GN=Vars1 PE=1 SV=1
Q04462	Valine--tRNA ligase OS=Rattus norvegicus OX=10116 GN=Vars1 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002928 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00133 all species →	tRNA-synt_1	tRNA synthetases class I (I, L, M and V)	Domain	Interproscan
PF08264 all species →	Anticodon_1	Anticodon-binding domain of tRNA ligase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002303 all species →	Family	Valine-tRNA ligase	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR009080 all species →	Homologous_superfamily	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Interproscan
IPR002300 all species →	Domain	Aminoacyl-tRNA synthetase, class Ia	Interproscan
IPR009008 all species →	Homologous_superfamily	Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain	Interproscan
IPR013155 all species →	Domain	Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding	Interproscan
IPR037118 all species →	Homologous_superfamily	Valyl-tRNA synthetase, tRNA-binding arm superfamily	Interproscan
IPR001412 all species →	Conserved_site	Aminoacyl-tRNA synthetase, class I, conserved site	Interproscan
IPR033705 all species →	Domain	Valyl tRNA synthetase, anticodon-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11946 all species →	VALYL-TRNA SYNTHETASES	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0004832 all species →	Molecular Function	valine-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006438 all species →	Biological Process	valyl-tRNA aminoacylation	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0006418 all species →	Biological Process	tRNA aminoacylation for protein translation	Interproscan
GO:0002161 all species →	Molecular Function	aminoacyl-tRNA editing 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
K01873	VARS, valS; valyl-tRNA synthetase	EC:6.1.1.9	Transfer RNA biogenesis	ko03016	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_066910854.1 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

134.9Max TPM

66.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Mature medusa	5	5	74.51	93.65
medusa · Experiment Condition A1	4	4	64.55	66.54
medusa · Experiment Condition A2	4	4	48.42	51.73
medusa · Experiment Condition A3	4	4	5.89	7.57
Early gastrula	2	2	88.16	89.74
Planula 24hpf	2	2	131.21	134.89
Planula 48hpf	2	2	108.55	124.44
Planula 72hpf	2	2	78.39	88.64
Primary polyp	2	2	77.66	77.98
Gastrozooid	2	2	47.98	53.63
Gonozooid	2	2	79.53	86.10
Stolon	2	2	90.01	96.61
Baby medusa	2	2	43.11	44.93
medusa · Experiment Condition B1	2	2	54.10	59.25
medusa · Experiment Condition B2	2	2	66.19	70.52
Mixed	1	1	80.56	80.56

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	93.65
ERR2816250	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	83.93
ERR2862245	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	66.07
ERR2816249	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	65.53
ERR2816248	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	63.38
ERR3299478	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	66.54
ERR3299477	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	65.87
ERR3299475	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	64.32
ERR3299476	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	61.47
ERR3299481	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	51.73
ERR3299482	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	51.65
ERR3299479	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	46.18
ERR3299480	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	44.11
ERR3299484	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	7.57
ERR3299483	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	6.65
ERR3299486	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	4.97
ERR3299485	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	4.39
ERR2816230	Early gastrula	not recorded	Early gastrula	not recorded	ERP110164	89.74
ERR2816231	Early gastrula	not recorded	Early gastrula	not recorded	ERP110164	86.58
ERR2816233	Planula 24hpf	not recorded	Planula 24hpf	not recorded	ERP110164	134.89
ERR2816232	Planula 24hpf	not recorded	Planula 24hpf	not recorded	ERP110164	127.52
ERR2816235	Planula 48hpf	not recorded	Planula 48hpf	not recorded	ERP110164	124.44
ERR2816234	Planula 48hpf	not recorded	Planula 48hpf	not recorded	ERP110164	92.65
ERR2816236	Planula 72hpf	not recorded	Planula 72hpf	not recorded	ERP110164	88.64
ERR2816237	Planula 72hpf	not recorded	Planula 72hpf	not recorded	ERP110164	68.15
ERR2816238	Primary polyp	not recorded	Primary polyp	not recorded	ERP110164	77.98
ERR2816239	Primary polyp	not recorded	Primary polyp	not recorded	ERP110164	77.35
ERR2816241	Gastrozooid	not recorded	Gastrozooid	not recorded	ERP110164	53.63
ERR2816240	Gastrozooid	not recorded	Gastrozooid	not recorded	ERP110164	42.33
ERR2816242	Gonozooid	not recorded	Gonozooid	not recorded	ERP110164	86.10
ERR2816243	Gonozooid	not recorded	Gonozooid	not recorded	ERP110164	72.96
ERR2816245	Stolon	not recorded	Stolon	not recorded	ERP110164	96.61
ERR2816244	Stolon	not recorded	Stolon	not recorded	ERP110164	83.42
ERR2816247	Baby medusa	not recorded	Baby medusa	not recorded	ERP110164	44.93
ERR2816246	Baby medusa	not recorded	Baby medusa	not recorded	ERP110164	41.28
ERR3299472	medusa · Experiment Condition B1	not recorded	medusa	Experiment Condition B1	ERP115020	59.25
ERR3299471	medusa · Experiment Condition B1	not recorded	medusa	Experiment Condition B1	ERP115020	48.95
ERR3299474	medusa · Experiment Condition B2	not recorded	medusa	Experiment Condition B2	ERP115020	70.52
ERR3299473	medusa · Experiment Condition B2	not recorded	medusa	Experiment Condition B2	ERP115020	61.87
ERR2862244	Mixed	not recorded	Mixed	not recorded	ERP110164	80.56

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	33	XP_066928397.1	0.950109458845222
Negatively correlated	41	XP_066935013.1	-0.85805172474764

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 →