Gene detail

Detailed information of HSymV2.0_g02.03949_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_2:28572636...28575408
NR annotation: XP_002157151.1, 60S ribosomal protein L4-B [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
Q9D8E6	Large ribosomal subunit protein uL4 OS=Mus musculus OX=10090 GN=Rpl4 PE=1 SV=3
P02385	Large ribosomal subunit protein uL4B OS=Xenopus laevis OX=8355 GN=rpl4-b PE=1 SV=2
P50878	Large ribosomal subunit protein uL4 OS=Rattus norvegicus OX=10116 GN=Rpl4 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006090 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14374 all species →	Ribos_L4_asso_C	60S ribosomal protein L4 C-terminal domain	Domain	Interproscan
PF00573 all species →	Ribosomal_L4	Ribosomal protein L4/L1 family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR025755 all species →	Domain	Large ribosomal subunit protein uL4, C-terminal domain	Interproscan
IPR023574 all species →	Homologous_superfamily	Large ribosomal subunit protein uL4 domain superfamily	Interproscan
IPR013000 all species →	Conserved_site	Large ribosomal subunit protein uL4, eukaryotic/archaeal, conserved site	Interproscan
IPR045240 all species →	Family	Large ribosomal subunit protein uL4, eukaryotic and archaeal type	Interproscan
IPR002136 all species →	Family	Large ribosomal subunit protein uL4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19431 all species →	60S RIBOSOMAL PROTEIN L4	Interproscan

Gene Ontology

GO term	Category	Description	Source
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:0003723 all species →	Molecular Function	RNA binding	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
K02930	RP-L4e, RPL4; large subunit ribosomal protein L4e	-	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_g02.03949_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

4,345.4Max TPM

843.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	894.29	4,345.36
Whole embryo · Triptolide 20 uM	4	4	492.17	564.04
Whole embryo · DMSO 0.5%	4	4	741.85	932.28

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
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	4,345.36
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	3,289.34
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	3,247.90
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	3,040.30
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	2,814.37
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	2,148.34
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	1,011.88
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	866.96
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	820.47
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	709.96
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	537.07
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	471.91
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	464.34
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	450.95
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	435.16
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	426.78
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	415.46
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	411.07
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	408.34
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	404.95
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	384.99
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	383.73
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	371.77
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	369.44
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	365.11
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	361.12
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	358.41
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	356.74
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	329.96
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	321.43
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	315.39
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	315.35
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	315.29
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	310.14
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	307.62
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	307.15
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	564.04
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	560.92
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	427.52
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	416.18
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	932.28
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	772.61
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	685.61
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	576.92

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	26	HSymV2.0_g05.08009_t1	0.989528589013356
Negatively correlated	21	HSymV2.0_g12.21085_t1	-0.948936971155493

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 →