Gene detail

Detailed information of HSymV2.0_g07.11929_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_7:10486382...10487231
NR annotation: XP_002164458.1, H/ACA ribonucleoprotein complex subunit 2-like protein [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
Q6NTV9	H/ACA ribonucleoprotein complex subunit 2-like protein OS=Xenopus laevis OX=8355 GN=nhp2 PE=2 SV=1
Q6P8C4	H/ACA ribonucleoprotein complex subunit 2-like protein OS=Xenopus tropicalis OX=8364 GN=nhp2 PE=2 SV=1
Q5RC65	H/ACA ribonucleoprotein complex subunit 2 OS=Pongo abelii OX=9601 GN=NHP2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007293 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01248 all species →	Ribosomal_L7Ae	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029064 all species →	Homologous_superfamily	Ribosomal protein eL30-like superfamily	Interproscan
IPR018492 all species →	Family	Ribosomal protein eL8/Nhp2 family	Interproscan
IPR050257 all species →	Family	Eukaryotic ribosomal RNA-processing and assembly protein	Interproscan
IPR002415 all species →	Family	H/ACA ribonucleoprotein complex, subunit Nhp2-like	Interproscan
IPR004038 all species →	Domain	Ribosomal protein eL8/eL30/eS12/Gadd45	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23105 all species →	RIBOSOMAL PROTEIN L7AE FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000469 all species →	Biological Process	obsolete cleavage involved in rRNA processing	Interproscan
GO:0000470 all species →	Biological Process	maturation of LSU-rRNA	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0022625 all species →	Cellular Component	cytosolic large ribosomal subunit	Interproscan
GO:0031118 all species →	Biological Process	rRNA pseudouridine synthesis	Interproscan
GO:0031120 all species →	Biological Process	snRNA pseudouridine synthesis	Interproscan
GO:0031429 all species →	Cellular Component	box H/ACA snoRNP complex	Interproscan
GO:0034513 all species →	Molecular Function	box H/ACA snoRNA binding	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	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
K11129	NHP2, NOLA2; H/ACA ribonucleoprotein complex subunit 2	-	DNA replication proteins	ko03032	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_g07.11929_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

293.6Max TPM

175.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	163.27	277.33
Whole embryo · Triptolide 20 uM	4	4	221.27	263.73
Whole embryo · DMSO 0.5%	4	4	240.14	293.59

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
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	277.33
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	261.35
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	222.81
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	205.05
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	202.27
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	197.16
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	190.00
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	186.46
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	180.34
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	175.73
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	174.04
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	172.90
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	172.16
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	163.52
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	163.03
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	160.62
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	158.73
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	155.57
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	155.00
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	154.53
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	153.08
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	150.16
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	148.75
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	148.75
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	148.41
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	139.14
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	139.00
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	137.95
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	135.02
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	133.95
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	133.85
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	132.32
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	126.71
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	123.32
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	118.51
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	80.20
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	263.73
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	242.59
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	198.85
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	179.91
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	293.59
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	274.76
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	207.77
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	184.45

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	28	HSymV2.0_g09.17327_t1	0.938534899380562
Negatively correlated	10	HSymV2.0_g09.14934_t1	-0.828955922509352

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 →