Gene detail

Detailed information of HSymV2.0_g03.05239_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_3:19878983...19886162
NR annotation: XP_002158217.1, 60S ribosomal protein L8 [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
Q9V3G1	Large ribosomal subunit protein uL2 OS=Drosophila melanogaster OX=7227 GN=RpL8 PE=1 SV=1
Q6RYS3	Large ribosomal subunit protein uL2 OS=Mamestra brassicae OX=55057 GN=RpL8 PE=2 SV=1
Q95V39	Large ribosomal subunit protein uL2 OS=Spodoptera frugiperda OX=7108 GN=RpL8 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007403 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00181 all species →	Ribosomal_L2	Ribosomal Proteins L2, RNA binding domain	Domain	Interproscan
PF03947 all species →	Ribosomal_L2_C	Ribosomal Proteins L2, C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002171 all species →	Family	Large ribosomal subunit protein uL2	Interproscan
IPR014722 all species →	Homologous_superfamily	Large ribosomal subunit protein uL2, domain 2	Interproscan
IPR022671 all species →	Conserved_site	Large ribosomal subunit protein uL2, conserved site	Interproscan
IPR022666 all species →	Domain	Large ribosomal subunit protein uL2, RNA-binding domain	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR008991 all species →	Homologous_superfamily	Translation protein SH3-like domain superfamily	Interproscan
IPR022669 all species →	Domain	Large ribosomal subunit protein uL2, C-terminal	Interproscan
IPR014726 all species →	Homologous_superfamily	Large ribosomal subunit protein uL2, domain 3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13691 all species →	RIBOSOMAL PROTEIN L2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0002181 all species →	Biological Process	cytoplasmic translation	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	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
GO:0022625 all species →	Cellular Component	cytosolic large ribosomal subunit	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
K02938	RP-L8e, RPL8; large subunit ribosomal protein L8e	-	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_g03.05239_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

4,387.8Max TPM

923.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	975.83	4,387.76
Whole embryo · Triptolide 20 uM	4	4	666.97	833.96
Whole embryo · DMSO 0.5%	4	4	704.26	916.35

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	4,387.76
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	3,627.50
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	3,369.76
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	2,945.76
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	2,363.31
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	1,952.87
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	799.17
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	786.67
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	742.27
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	736.91
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	721.48
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	707.61
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	702.73
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	672.99
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	660.21
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	562.07
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	557.69
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	554.24
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	545.88
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	542.84
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	529.01
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	523.09
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	513.11
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	511.65
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	504.96
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	503.18
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	502.01
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	486.06
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	471.65
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	423.17
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	395.89
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	383.78
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	372.40
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	364.20
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	362.29
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	343.62
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	833.96
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	791.11
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	530.35
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	512.47
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	916.35
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	819.78
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	560.19
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	520.74

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	29	HSymV2.0_g08.13833_t1	0.996583605406017
Negatively correlated	12	HSymV2.0_g05.09506_t1	-0.953772523992399

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 →