Gene detail

Detailed information of HSymV2.0_g10.18183_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_10:11703070...11704171
NR annotation: XP_047134745.1, DNA repair protein RAD51 homolog A [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
Q8MKI8	DNA repair protein RAD51 homolog 1 OS=Canis lupus familiaris OX=9615 GN=RAD51 PE=2 SV=1
Q06609	DNA repair protein RAD51 homolog 1 OS=Homo sapiens OX=9606 GN=RAD51 PE=1 SV=1
Q91918	DNA repair protein RAD51 homolog A OS=Xenopus laevis OX=8355 GN=rad51-a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001814 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14520 all species →	HHH_5	Helix-hairpin-helix domain	Domain	Interproscan
PF08423 all species →	Rad51	Rad51	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR013632 all species →	Domain	DNA recombination and repair protein Rad51-like, C-terminal	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR011941 all species →	Family	DNA recombination/repair protein Rad51	Interproscan
IPR020587 all species →	Domain	DNA recombination and repair protein RecA, monomer-monomer interface	Interproscan
IPR010995 all species →	Homologous_superfamily	DNA repair Rad51/transcription factor NusA, alpha-helical	Interproscan
IPR020588 all species →	Domain	DNA recombination and repair protein RecA-like, ATP-binding domain	Interproscan
IPR016467 all species →	Family	DNA recombination and repair protein, RecA-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22942 all species →	RECA/RAD51/RADA DNA STRAND-PAIRING FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000150 all species →	Molecular Function	DNA strand exchange activity	Interproscan
GO:0000730 all species →	Biological Process	DNA recombinase assembly	Interproscan
GO:0000794 all species →	Cellular Component	condensed nuclear chromosome	Interproscan
GO:0003690 all species →	Molecular Function	double-stranded DNA binding	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0006312 all species →	Biological Process	mitotic recombination	Interproscan
GO:0007131 all species →	Biological Process	reciprocal meiotic recombination	Interproscan
GO:0008094 all species →	Molecular Function	ATP-dependent activity, acting on DNA	Interproscan
GO:0042148 all species →	Biological Process	DNA strand invasion	Interproscan
GO:0070192 all species →	Biological Process	chromosome organization involved in meiotic cell cycle	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:1990426 all species →	Biological Process	mitotic recombination-dependent replication fork processing	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006259 all species →	Biological Process	DNA metabolic process	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor activity	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
K04482	RAD51; DNA repair protein RAD51	-	DNA repair and recombination proteins	ko03400	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_g10.18183_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

134.4Max TPM

77.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	81.76	134.42
Whole embryo · Triptolide 20 uM	4	4	65.43	85.05
Whole embryo · DMSO 0.5%	4	4	53.35	60.49

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
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	134.42
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	115.38
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	110.78
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	109.99
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	109.45
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	107.33
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	106.22
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	104.36
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	101.82
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	99.87
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	99.30
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	98.98
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	98.28
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	97.65
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	93.94
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	92.81
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	92.75
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	90.01
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	89.74
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	89.74
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	89.42
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	89.07
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	87.31
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	84.55
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	83.11
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	77.21
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	66.43
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	59.19
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	57.89
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	51.27
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	33.29
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	27.10
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	25.59
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	24.28
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	23.87
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	21.06
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	85.05
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	67.27
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	62.29
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	47.09
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	60.49
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	54.28
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	51.72
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	46.91

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	23	HSymV2.0_g08.13523_t1	0.9602524565954
Negatively correlated	5	HSymV2.0_g11.19594_t1	-0.879516590571596

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 →