Gene detail

Detailed information of HSymV2.0_g08.13657_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_8:11843089...11847097
NR annotation: XP_004211786.1, 40S ribosomal protein S3a [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
A7S3J7	Small ribosomal subunit protein eS1 OS=Nematostella vectensis OX=45351 GN=v1g242621 PE=3 SV=1
P49242	Small ribosomal subunit protein eS1 OS=Rattus norvegicus OX=10116 GN=Rps3a PE=1 SV=2
B5FZS9	Small ribosomal subunit protein eS1 OS=Taeniopygia guttata OX=59729 GN=RPS3A PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007928 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01015 all species →	Ribosomal_S3Ae	Ribosomal S3Ae family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001593 all species →	Family	Small ribosomal subunit protein eS1	Interproscan
IPR027500 all species →	Family	Small ribosomal subunit protein eS1, eukaryotes	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11830 all species →	40S RIBOSOMAL PROTEIN S3A	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0005840 all species →	Cellular Component	ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	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
K02984	RP-S3Ae, RPS3A; small subunit ribosomal protein S3Ae	-	Ribosome	ko03011	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_g08.13657_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

5,232.9Max TPM

1,053.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	1,114.89	5,232.90
Whole embryo · Triptolide 20 uM	4	4	728.33	874.01
Whole embryo · DMSO 0.5%	4	4	824.24	1,064.11

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
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	5,232.90
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	5,033.86
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	3,982.78
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	3,945.53
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	3,251.93
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	2,586.93
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	1,078.87
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	980.17
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	793.72
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	701.03
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	678.31
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	661.62
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	661.02
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	657.27
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	639.73
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	633.10
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	599.84
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	598.33
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	538.00
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	536.38
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	529.95
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	510.83
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	492.09
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	456.80
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	434.66
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	431.69
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	431.32
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	430.63
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	411.27
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	374.64
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	321.87
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	321.06
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	304.48
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	303.62
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	300.12
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	289.78
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	874.01
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	869.92
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	592.84
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	576.54
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	1,064.11
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	945.94
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	673.36
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	613.57

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	31	HSymV2.0_g07.12036_t1	0.997437341830222
Negatively correlated	12	HSymV2.0_g05.09506_t1	-0.959231453185094

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 →