Gene detail

Detailed information of HSymV2.0_g06.10954_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_6:22317008...22318686
NR annotation: XP_002160475.1, exosome complex component RRP41 [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
Q7YRA3	Exosome complex component RRP41 OS=Bos taurus OX=9913 GN=EXOSC4 PE=2 SV=3
Q921I9	Exosome complex component RRP41 OS=Mus musculus OX=10090 GN=Exosc4 PE=1 SV=3
Q9NPD3	Exosome complex component RRP41 OS=Homo sapiens OX=9606 GN=EXOSC4 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001803 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01138 all species →	RNase_PH	3' exoribonuclease family, domain 1	Domain	Interproscan
PF03725 all species →	RNase_PH_C	3' exoribonuclease family, domain 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001247 all species →	Domain	Exoribonuclease, phosphorolytic domain 1	Interproscan
IPR050080 all species →	Family	Ribonuclease PH	Interproscan
IPR020568 all species →	Homologous_superfamily	Ribosomal protein uS5 domain 2-type superfamily	Interproscan
IPR015847 all species →	Domain	Exoribonuclease, phosphorolytic domain 2	Interproscan
IPR036345 all species →	Homologous_superfamily	Exoribonuclease, PH domain 2 superfamily	Interproscan
IPR027408 all species →	Homologous_superfamily	PNPase/RNase PH domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11953 all species →	EXOSOME COMPLEX COMPONENT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000176 all species →	Cellular Component	nuclear exosome (RNase complex)	Interproscan
GO:0000177 all species →	Cellular Component	cytoplasmic exosome (RNase complex)	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0016075 all species →	Biological Process	rRNA catabolic process	Interproscan
GO:0034427 all species →	Biological Process	obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'	Interproscan
GO:0034475 all species →	Biological Process	U4 snRNA 3'-end processing	Interproscan
GO:0071028 all species →	Biological Process	nuclear mRNA surveillance	Interproscan
GO:0071051 all species →	Biological Process	poly(A)-dependent snoRNA 3'-end processing	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
K11600	RRP41, EXOSC4, SKI6; exosome complex component RRP41	-	Messenger RNA biogenesis	ko03019	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_g06.10954_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

204.2Max TPM

154.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	151.98	204.23
Whole embryo · Triptolide 20 uM	4	4	178.82	198.84
Whole embryo · DMSO 0.5%	4	4	157.43	182.46

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
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	204.23
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	202.06
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	199.10
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	194.49
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	193.03
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	192.70
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	189.07
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	188.51
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	187.16
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	186.34
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	186.20
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	185.31
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	183.59
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	181.70
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	179.16
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	179.12
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	177.43
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	174.68
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	174.25
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	174.22
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	173.84
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	169.20
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	167.79
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	166.61
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	165.66
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	159.70
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	155.27
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	152.99
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	146.01
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	131.38
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	36.41
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	32.80
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	25.04
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	22.28
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	19.91
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	13.89
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	198.84
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	185.27
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	170.94
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	160.24
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	182.46
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	171.72
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	145.58
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	129.97

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	35	HSymV2.0_g01.00021_t1	0.960689359451324
Negatively correlated	130	HSymV2.0_g08.13158_t1	-0.958593802654012

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 →