Gene detail

Detailed information of XP_065663526.1 in Hydra vulgaris

Genomic Location: NC_088929.1:20194909...20276821
NR annotation: XP_047141686.1, replication protein A 70 kDa DNA-binding subunit [Hydra vulgaris]
Species Hydra vulgaris · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_065807454.1

AACAAAAATATGACCATACTACCGTTGAAAAATGTCGGTTTGTAAATCGGTTCCCTCGTCGTAATTTCGCTATTATGTTAGCTAGTTTGTGTTCGTTTCCCGCTTTAATTTCAGTTTAATTTTAACAGCGAAATTTTAACAAGAAACTGAAGAATGTCACTTACAGCTGGTGCTATTCAGGCTATTATCACTGCTCCAGACCATGAACATATGCCTGTTCAACCTGTAGTTCAAATATTGgggATAAAAAAGTTACAGGCTGGTCCTGGTGCAAATGAGAGATACCGcttgGTTTTATCAGATGGAGAACATTATTACACTtCTGCCATGCTGGGCACACAATTAAATGATACAGTACAGGAAGATATGGTAGAGGTGAGATGTGTATTACAGATGGATAAATATACCTGCAATGTGATTCAGGGTACTAGgAAAGTCATTATCATTCTTGAactaaagataatattaaaagcaTCTGAGGTCCCTGGAAAAATTGGAGAACCAGTACAGATATCTGATTTGTTAACGGAACAAGAAAATCTTCTACCACTGCctattaaaaaagaaactgtCAATAGTAGCTCAAAActgcaaaatatttcaaatcaaattaaatcTGCTTCAACAAATAATAcaaAAAATCTACCTGTTCCAAACAAGCCTTTGTCAAATCAAAAACCATCTGCTTATTCAGCAGCCAATCAAAAACCACCTGGGTATTCAACAGCAGGAGCAGGaagtgTTGTTGACTCAAATTCGAAATCAGTGTTCCCAATCTCATCATTAACACCATATCAAAACAgGTGGACAATTCGTGCGCGAATAACAAACAAATCACCTATTCGTACATGGAGTAATTCCAGAGGAGATGGAAAACTTTTCAGTATAGACCTTGTTGATGAATCGGGGGAAATACGTGCAACTGCTTTCAATGAAGTTGTAGATAAATATTATGATTTACTGGAAATTGGAAAgGTCTACTATATCACAAAAGGATCATTAAAGACAGCTAATAAACAATACAGTTCTTTAAAGAATGATTATGAGATGACATTAAATAATGACTCTTTAGTCGAGctttGTAATGATTTGTGTGATTTACCAACATTGCAgtttaatttcaaacaaattaagTCTATTGAAGATGTAAACAAAGATGCTTTGATAGaTGTTGTTGGAATAGTTAAAAGTTCTTCTGAAATGCAGCAAATAACAACTAAAGCAACTAATAAACAAGTTTGGAAGCGAGATATAACAATTGTTGATCAATCAGGTTCGGCTGTACAAGCTACAATATGGGGTAGTGAGGCTGAAAAGTTTGAAGAGTACACAGATAAGAATCCTGTTGTTGCAATCAAAGGTGCTAAAGTATCTGATTTTGGAGGTCGATCACTGTCAATCTTAAATTCAAGTATTTTTCATATTAATCCTGATATACCTGAAGCTTTTGAGTTGAGAGGatggtTTGATAATGGGGGAGTTAATGAACAAACAACTTCAATATCTGGACAAAGAATGGAGGGAGCAGGTGGTGGAAAGTATAAAACTCTTGGTCAAATAAAAGATGAAGGTCTTGGTATGGGAGAAAAGccTGATTATTTCAATGTGCGTGCATTCGTTGTATTTTATCGTAAAGAAAATTGCATGTATCAAGCCTGTCCTGGTGCTGATTGTAATAAGAAAGTCATTGAAGATAATGGCCAGTTCAGATGTGAAAAATGTGATCGGACATACCCAGATTTTAAATATCGAATGGTTTTGTCGgcAAATATTGCTGATTTCTCAGGTAATCAATGGATTACAGCTTTTCAAGAGAGTGCTGAGGCTATTTTAGGTGTTTCTGCTGAGCAAGTTGGTCAATTAAAAGATACGgacGTGTCTCAATTTGATATGATTTTTAGTGAAGCTTGTTTCAAACCTTTTGTGTTTAAAGTTCGTGCAAAGATGGAGACTTATCAGGatgaaagaaaacttaaatgttcCGCTGTGTCTGCAGCGCCAGTTAACTTCAAACAAGAATGCAAAAGACTTATAgacgaaataaaaaatcttgaaagaCTATAGCTTAAAAGTTTGAGACTTCTGTGACGAATAAGCAACACGAAGACGTCAGTTATGTACAAACACTCTTGATGTAAAGCAATTTAATAAACATCGTGTAATTATCTAAAAACATATGGATGGAGTTAAAGTTATTTAACGCCTAATTCGTTTTTGTTTATAGATAagtaaaaaacattctttaaatCATATGctgataattttgtttagaGATGTCTGTTTAATTATGCtatgtatttttgtattgtttagcaaaataacacaaaaacatgtttta

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P27694	Replication protein A 70 kDa DNA-binding subunit OS=Homo sapiens OX=9606 GN=RPA1 PE=1 SV=2
Q5R7Q4	Replication protein A 70 kDa DNA-binding subunit OS=Pongo abelii OX=9601 GN=RPA1 PE=2 SV=1
Q8VEE4	Replication protein A 70 kDa DNA-binding subunit OS=Mus musculus OX=10090 GN=Rpa1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004288 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04057 all species →	Rep-A_N	Replication factor-A protein 1, N-terminal domain	Domain	Interproscan
PF01336 all species →	tRNA_anti-codon	OB-fold nucleic acid binding domain	Domain	Interproscan
PF08646 all species →	Rep_fac-A_C	Replication factor-A C terminal domain	Family	Interproscan
PF16900 all species →	REPA_OB_2	Replication protein A OB domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR004591 all species →	Family	Replication factor A protein 1	Interproscan
IPR007199 all species →	Domain	Replication factor-A protein 1, N-terminal	Interproscan
IPR004365 all species →	Domain	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Interproscan
IPR047192 all species →	Domain	Replication factor A, C-terminal, eukaryotes	Interproscan
IPR013955 all species →	Domain	Replication factor A, C-terminal	Interproscan
IPR031657 all species →	Domain	Replication protein A, OB domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23273 all species →	REPLICATION FACTOR A 1, RFA1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0005662 all species →	Cellular Component	DNA replication factor A complex	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0007004 all species →	Biological Process	telomere maintenance via telomerase	Interproscan
GO:0043047 all species →	Molecular Function	single-stranded telomeric DNA binding	Interproscan
GO:0051321 all species →	Biological Process	meiotic cell cycle	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
K07466	RFA1, RPA1, rpa; replication factor A1	-	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 XP_065663526.1 across 60 RNA-seq samples of Hydra vulgaris. 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.

60Samples

60TPM > 0

8Conditions

104.6Max TPM

79.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Regenerating head · dmso treatment	18	18	76.73	97.20
Regenerating head · 25uM U0126 treatment	15	15	75.88	94.81
Regenerating foot · dmso treatment	9	9	85.57	104.64
Regenerating foot · 25uM U0126 treatment	8	8	86.92	95.19
Regenerating head · u0126 treatment	3	3	79.22	80.14
Whole animal · 25uM U0126 treatment	3	3	82.55	85.35
Whole animal · dmso treatment	3	3	78.59	82.68
Regenerating foot · u0126 treatment	1	1	80.05	80.05

Per sample · hover a bar for the full sample record

Show the sample table (60 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR36435285	Regenerating head · dmso treatment	Regenerating head	0hpa	dmso treatment	SRP654941	97.20
SRR36435284	Regenerating head · dmso treatment	Regenerating head	0hpa	dmso treatment	SRP654941	92.58
SRR36435286	Regenerating head · dmso treatment	Regenerating head	0hpa	dmso treatment	SRP654941	85.97
SRR36435308	Regenerating head · dmso treatment	Regenerating head	3hpa	dmso treatment	SRP654941	81.64
SRR36435306	Regenerating head · dmso treatment	Regenerating head	1.5hpa	dmso treatment	SRP654941	81.29
SRR36435309	Regenerating head · dmso treatment	Regenerating head	3hpa	dmso treatment	SRP654941	80.55
SRR36435279	Regenerating head · dmso treatment	Regenerating head	8hpa	dmso treatment	SRP654941	79.74
SRR36435272	Regenerating head · dmso treatment	Regenerating head	12hpa	dmso treatment	SRP654941	79.52
SRR36435277	Regenerating head · dmso treatment	Regenerating head	8hpa	dmso treatment	SRP654941	78.86
SRR36435307	Regenerating head · dmso treatment	Regenerating head	3hpa	dmso treatment	SRP654941	77.11
SRR36435280	Regenerating head · dmso treatment	Regenerating head	8hpa	dmso treatment	SRP654941	75.49
SRR36435304	Regenerating head · dmso treatment	Regenerating head	1.5hpa	dmso treatment	SRP654941	74.67
SRR36435305	Regenerating head · dmso treatment	Regenerating head	1.5hpa	dmso treatment	SRP654941	73.24
SRR36435313	Regenerating head · dmso treatment	Regenerating head	0hpa	dmso treatment	SRP654941	71.60
SRR36435273	Regenerating head · dmso treatment	Regenerating head	12hpa	dmso treatment	SRP654941	68.42
SRR36435310	Regenerating head · dmso treatment	Regenerating head	0hpa	dmso treatment	SRP654941	67.43
SRR36435271	Regenerating head · dmso treatment	Regenerating head	12hpa	dmso treatment	SRP654941	61.96
SRR36435312	Regenerating head · dmso treatment	Regenerating head	0hpa	dmso treatment	SRP654941	53.85
SRR36435281	Regenerating head · 25uM U0126 treatment	Regenerating head	0hpa	25uM U0126 treatment	SRP654941	94.81
SRR36435303	Regenerating head · 25uM U0126 treatment	Regenerating head	0hpa	25uM U0126 treatment	SRP654941	85.83
SRR36435275	Regenerating head · 25uM U0126 treatment	Regenerating head	8hpa	25uM U0126 treatment	SRP654941	85.65
SRR36435299	Regenerating head · 25uM U0126 treatment	Regenerating head	3hpa	25uM U0126 treatment	SRP654941	81.06
SRR36435298	Regenerating head · 25uM U0126 treatment	Regenerating head	3hpa	25uM U0126 treatment	SRP654941	79.99
SRR36435296	Regenerating head · 25uM U0126 treatment	Regenerating head	1.5hpa	25uM U0126 treatment	SRP654941	79.66
SRR36435282	Regenerating head · 25uM U0126 treatment	Regenerating head	0hpa	25uM U0126 treatment	SRP654941	79.18
SRR36435295	Regenerating head · 25uM U0126 treatment	Regenerating head	1.5hpa	25uM U0126 treatment	SRP654941	76.12
SRR36435294	Regenerating head · 25uM U0126 treatment	Regenerating head	1.5hpa	25uM U0126 treatment	SRP654941	73.75
SRR36435302	Regenerating head · 25uM U0126 treatment	Regenerating head	0hpa	25uM U0126 treatment	SRP654941	72.97
SRR36435283	Regenerating head · 25uM U0126 treatment	Regenerating head	0hpa	25uM U0126 treatment	SRP654941	71.15
SRR36435301	Regenerating head · 25uM U0126 treatment	Regenerating head	0hpa	25uM U0126 treatment	SRP654941	68.53
SRR36435276	Regenerating head · 25uM U0126 treatment	Regenerating head	8hpa	25uM U0126 treatment	SRP654941	65.73
SRR36435297	Regenerating head · 25uM U0126 treatment	Regenerating head	3hpa	25uM U0126 treatment	SRP654941	63.42
SRR36435274	Regenerating head · 25uM U0126 treatment	Regenerating head	8hpa	25uM U0126 treatment	SRP654941	60.41
SRR36435300	Regenerating foot · dmso treatment	Regenerating foot	3hpa	dmso treatment	SRP654941	104.64
SRR36435289	Regenerating foot · dmso treatment	Regenerating foot	3hpa	dmso treatment	SRP654941	96.71
SRR36435265	Regenerating foot · dmso treatment	Regenerating foot	1.5hpa	dmso treatment	SRP654941	90.93
SRR36435267	Regenerating foot · dmso treatment	Regenerating foot	1.5hpa	dmso treatment	SRP654941	87.54
SRR36435278	Regenerating foot · dmso treatment	Regenerating foot	3hpa	dmso treatment	SRP654941	87.19
SRR36435266	Regenerating foot · dmso treatment	Regenerating foot	1.5hpa	dmso treatment	SRP654941	82.39
SRR36435322	Regenerating foot · dmso treatment	Regenerating foot	0hpa	dmso treatment	SRP654941	80.81
SRR36435323	Regenerating foot · dmso treatment	Regenerating foot	0hpa	dmso treatment	SRP654941	78.20
SRR36435311	Regenerating foot · dmso treatment	Regenerating foot	0hpa	dmso treatment	SRP654941	61.75
SRR36435314	Regenerating foot · 25uM U0126 treatment	Regenerating foot	1.5hpa	25uM U0126 treatment	SRP654941	95.19
SRR36435318	Regenerating foot · 25uM U0126 treatment	Regenerating foot	3hpa	25uM U0126 treatment	SRP654941	95.02
SRR36435319	Regenerating foot · 25uM U0126 treatment	Regenerating foot	3hpa	25uM U0126 treatment	SRP654941	91.43
SRR36435321	Regenerating foot · 25uM U0126 treatment	Regenerating foot	0hpa	25uM U0126 treatment	SRP654941	85.37
SRR36435320	Regenerating foot · 25uM U0126 treatment	Regenerating foot	0hpa	25uM U0126 treatment	SRP654941	84.95
SRR36435315	Regenerating foot · 25uM U0126 treatment	Regenerating foot	1.5hpa	25uM U0126 treatment	SRP654941	83.31
SRR36435316	Regenerating foot · 25uM U0126 treatment	Regenerating foot	1.5hpa	25uM U0126 treatment	SRP654941	82.14
SRR36435317	Regenerating foot · 25uM U0126 treatment	Regenerating foot	3hpa	25uM U0126 treatment	SRP654941	77.91
SRR36435269	Regenerating head · u0126 treatment	Regenerating head	12hpa	u0126 treatment	SRP654941	80.14
SRR36435270	Regenerating head · u0126 treatment	Regenerating head	12hpa	u0126 treatment	SRP654941	79.50
SRR36435268	Regenerating head · u0126 treatment	Regenerating head	12hpa	u0126 treatment	SRP654941	78.03
SRR36435287	Whole animal · 25uM U0126 treatment	Whole animal	12h	25uM U0126 treatment	SRP654941	85.35
SRR36435290	Whole animal · 25uM U0126 treatment	Whole animal	12h	25uM U0126 treatment	SRP654941	82.16
SRR36435288	Whole animal · 25uM U0126 treatment	Whole animal	12h	25uM U0126 treatment	SRP654941	80.13
SRR36435291	Whole animal · dmso treatment	Whole animal	12h	dmso treatment	SRP654941	82.68
SRR36435293	Whole animal · dmso treatment	Whole animal	12h	dmso treatment	SRP654941	80.96
SRR36435292	Whole animal · dmso treatment	Whole animal	12h	dmso treatment	SRP654941	72.11
SRR36435264	Regenerating foot · u0126 treatment	Regenerating foot	0hpa	u0126 treatment	SRP654941	80.05

Source: CnidoSite RNA-seq expression matrices (HVULG_TPM, StringTie quantification over 60 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 Hydra vulgaris 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	29	XP_065675441.1	0.906456102657854
Negatively correlated	10	XP_065657281.1	-0.841794169763005

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 Hydra vulgaris, 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.

Dataset	Tissue / stage	Cells	Cell types	This gene	Marker of
HVULG_siebert_atlas	Whole animals · Adult (whole animal)	25,438	42	not in this dataset	–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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.

Peak calls overlapping this gene

Assay	Sample	Peaks	Region
ChIP-seq	H3K27ac_whole_polyp_24hr_DMSO_control	1	Promoter (<=1kb) 1
	H3K4me2_regenerating_head_24hr	1	Intron 1
	H3K4me2_wholeAnimal	2	Intron 1 · Promoter (<=1kb) 1
	H3K4me3_regenerating_head_24hr	1	Intron 1
	H3K4me3_wholeAnimal	1	Intron 1
	H4K20me1_regenerating_tips_8hrs	1	Intron 1
	H4K20me1_whole_polyp_ALP_treated	4	Intron 3 · Exon 1

Browse the full epigenomic landscape of this species: ChIP-seq.

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 →