Gene detail

Detailed information of HSymV2.0_g07.11458_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_7:3859120...3862558
NR annotation: XP_002160406.1, NHP2-like protein 1 [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
Q6P8E9	NHP2-like protein 1 OS=Xenopus tropicalis OX=8364 GN=snu13 PE=2 SV=1
Q5XH16	NHP2-like protein 1 OS=Xenopus laevis OX=8355 GN=snu13 PE=2 SV=1
Q3B8S0	NHP2-like protein 1 OS=Bos taurus OX=9913 GN=SNU13 PE=2 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008693 (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
IPR004037 all species →	Conserved_site	Large ribosomal subunit protein eL8-like, conserved site	Interproscan
IPR002415 all species →	Family	H/ACA ribonucleoprotein complex, subunit Nhp2-like	Interproscan
IPR018492 all species →	Family	Ribosomal protein eL8/Nhp2 family	Interproscan
IPR029064 all species →	Homologous_superfamily	Ribosomal protein eL30-like superfamily	Interproscan
IPR004038 all species →	Domain	Ribosomal protein eL8/eL30/eS12/Gadd45	Interproscan
IPR050257 all species →	Family	Eukaryotic ribosomal RNA-processing and assembly protein	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0042254 all species →	Biological Process	ribosome biogenesis	Interproscan
GO:1990904 all species →	Cellular Component	ribonucleoprotein complex	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000470 all species →	Biological Process	maturation of LSU-rRNA	Interproscan
GO:0022625 all species →	Cellular Component	cytosolic large ribosomal subunit	Interproscan
GO:0030490 all species →	Biological Process	maturation of SSU-rRNA	Interproscan
GO:0031428 all species →	Cellular Component	box C/D methylation guide snoRNP complex	Interproscan
GO:0032040 all species →	Cellular Component	small-subunit processome	Interproscan
GO:0046540 all species →	Cellular Component	U4/U6 x U5 tri-snRNP complex	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	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
K12845	SNU13, NHP2L; U4/U6 small nuclear ribonucleoprotein SNU13	-	Ribosome biogenesis	ko03009	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_g07.11458_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

43TPM > 0

3Conditions

1,310.2Max TPM

252.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	35	258.25	1,310.18
Whole embryo · Triptolide 20 uM	4	4	173.82	225.07
Whole embryo · DMSO 0.5%	4	4	282.44	370.47

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	1,310.18
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	1,235.63
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	962.56
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	789.57
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	523.78
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	444.46
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	320.20
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	308.69
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	226.55
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	185.08
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	177.19
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	175.35
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	170.09
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	169.35
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	168.84
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	165.43
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	157.53
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	155.77
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	133.95
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	129.92
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	125.73
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	122.53
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	122.46
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	115.66
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	106.39
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	103.48
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	94.98
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	91.93
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	90.24
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	78.78
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	69.93
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	69.00
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	68.22
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	67.24
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	60.40
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	0.00
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	225.07
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	177.44
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	148.62
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	144.14
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	370.47
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	316.76
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	242.69
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	199.83

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	16	HSymV2.0_g04.06879_t1	0.993129498254742
Negatively correlated	6	HSymV2.0_g08.13615_t1	-0.931220986168101

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 →