Gene detail

Detailed information of HSymV2.0_g03.05153_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_3:17937765...17947511
NR annotation: XP_047130060.1, phenylalanine--tRNA ligase beta subunit isoform X1 [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
Q9WUA2	Phenylalanine--tRNA ligase beta subunit OS=Mus musculus OX=10090 GN=Farsb PE=1 SV=2
Q9NSD9	Phenylalanine--tRNA ligase beta subunit OS=Homo sapiens OX=9606 GN=FARSB PE=1 SV=3
Q5R7F7	Phenylalanine--tRNA ligase beta subunit OS=Pongo abelii OX=9601 GN=FARSB PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003624 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03484 all species →	B5	tRNA synthetase B5 domain	Domain	Interproscan
PF18262 all species →	PhetRS_B1	Phe-tRNA synthetase beta subunit B1 domain	Domain	Interproscan
PF03483 all species →	B3_4	B3/4 domain	Domain	Interproscan
PF17759 all species →	tRNA_synthFbeta	Phenylalanyl tRNA synthetase beta chain CLM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005147 all species →	Domain	tRNA synthetase, B5-domain	Interproscan
IPR040659 all species →	Domain	Phenylalanine--tRNA ligase beta subunit, B1 domain	Interproscan
IPR009061 all species →	Homologous_superfamily	Putative DNA-binding domain superfamily	Interproscan
IPR005146 all species →	Domain	B3/B4 tRNA-binding domain	Interproscan
IPR045864 all species →	Homologous_superfamily	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Interproscan
IPR041616 all species →	Domain	Phenylalanyl tRNA synthetase beta chain, core domain	Interproscan
IPR020825 all species →	Homologous_superfamily	Phenylalanyl-tRNA synthetase-like, B3/B4	Interproscan
IPR004531 all species →	Family	Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type	Interproscan
IPR045060 all species →	Family	Phenylalanine-tRNA ligase, class IIc, beta subunit	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10947 all species →	PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000287 all species →	Molecular Function	magnesium ion binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006432 all species →	Biological Process	phenylalanyl-tRNA aminoacylation	Interproscan
GO:0004826 all species →	Molecular Function	phenylalanine-tRNA ligase activity	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0009328 all species →	Cellular Component	phenylalanine-tRNA ligase complex	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
K01890	FARSB, pheT; phenylalanyl-tRNA synthetase beta chain	EC:6.1.1.20	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 HSymV2.0_g03.05153_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

43TPM > 0

3Conditions

132.6Max TPM

97.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	35	95.34	128.36
Whole embryo · Triptolide 20 uM	4	4	124.53	132.55
Whole embryo · DMSO 0.5%	4	4	94.09	97.55

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
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	128.36
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	121.53
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	119.72
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	119.17
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	119.12
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	117.54
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	116.05
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	115.44
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	113.07
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	112.33
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	110.05
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	109.97
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	109.53
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	108.96
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	108.20
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	106.91
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	105.18
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	103.32
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	103.13
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	101.34
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	100.82
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	98.74
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	95.07
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	93.93
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	86.43
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	85.31
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	84.64
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	80.73
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	79.70
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	76.91
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	72.50
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	69.85
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	60.22
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	51.95
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	46.65
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	0.00
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	132.55
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	129.36
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	124.77
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	111.46
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	97.55
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	95.22
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	94.15
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	89.44

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	22	HSymV2.0_g03.05969_t1	0.909903413214897
Negatively correlated	8	HSymV2.0_g03.04657_t1	-0.822442249824976

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 →