Gene detail

Detailed information of XP_048586397.1 in Nematostella vectensis

Genomic Location: NC_064040.1:8056523...8061103
NR annotation: XP_048586397.1, DNA repair protein XRCC3 isoform X2 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_048730440.1

CTAGTACCAGTCTCTTTCacaattcaagatggcggccgatGCCATTCGGCGGTCTTTTCAAACTTGACAAGCCCTTTTCATTGGTAACTCCTGGAGAAAACAAACAGTTGCCGTAATGCAATGACTAATTTGCCAAGAATATAAGCATGGAGAGGCTGGATCTACCACCGAGAATAATCAGTGCTTTGAGAAAAGCCCGCATATCCAGCATGCACCAAGTAATATGTATGTCCGCGGCAGATTTAGAGCGCAGCACAAAGCTATCAATCACAGATGTCCAACTTCTACAGCAAGTTGTCTCGGCTGTCATTCCACGACCACCCATGCAGTCTGCTCTGGAGATGTACCAGGATTGTTTGAGCGGTGGAAGGCGTGTCAGTGTAGGGTGTCCTGTCCTAGATAAGGTGCTGAAAGGGGGGCTTCTCTGTCATGGAATCACAGAGATCACAGGAGAGAGTGCATCTGgTGCCTTGTACATATCCACAGAAGATGTATTTCCCAGCAAACGTCTTCATCAACTCATCCCAAACTTTTTACAGGCCCTTCCAACACAAGTTGCTGCTCAGCTAAAGCTTGGAGACAATATCTTTATAGAGCATGCCTCAGATGTGGATGAGCTAAAGGACATCATCTATACTCGCTTACCAATTCTCCTAAGCCAGCGTAAAGTCCAGCTAGTGGTGATTGACTCTGTAACAGCACTATTCCGAGTGGAGTTTGGTTTAGGAGAGATGTCTTACCGTGGAAAAGTGTTGAGGTCATTTGGGGCTCAGTTGCACAAGCTTAGTCATGATTATCAAGTTGCTGTTGTTTGTGTTAATCAGGTTTCCGATGTTGTGAATGGCAGCAATACAGACAGGTTGCACAAAGTTATCCCAGCTTTGGGCCTAGCATGGTCTAGTATGGTCACTGTAAGGCTTATGCTCTCGCGCACAGAGGAGTATGTTCACAGTACAACAAGAATAGCTGACAAGCAAACTCTAGCCCCTGGTAAAGTGGTCAAGCGCTTGCTCTCAGTGGTGTTTGCACCTCATTTGCCAAGCAAATCCTGGCCATTTGTCGTCCAAGAGGATGGAGTACATGGCATCCAGGAAGAATCATAACATATGATGGTTCTTCCAAAATGTATACCAAGCCCTGTTCTAAAAGCTTTTATAAGCATTGCCAAACTTCACTGGAACCTCAATATAACAAGGGACAAAAAACATAATAAGGGATATCATTTTATTGAGGGAGGACCTGAAATTTATATTGTTAAACCAAGAGTATTGTTACAACTATTTCCCAGGTTTTCAAACCCAGCCTCATTTGTTTTGTGTAGAGAGAAGTAAGGGATGGGTAATGTGACAAAGTCTAGTTCCCAGTGCAGGATCAAAGAAACTGCAGAGCATACACTTTCCTAGAACTTTAGAAGTATATTTGTATGCTgttaaacaaatatttaaatgGAAGTGTATAGTtcaaagcaaaataaattataacGATTCTCAATACATCGTGACCCTTCACCTTGTAATGGTGATTTTGGTTATTTTTTGGACGTCAATCATCCACGTTTCCATAACGATCATGCAGACTTCATTTGTTTTGTGTATCAAAAGTTGTAGTCGACTTTACTCAGGGACACATTTGAAAACACAGTAAAGAAATGCAAAAGTTCAGTTCTcataaaaggataaaaaatgtattgcaaaacaTTCAAGCCTTGTTCCAAATGCTTTGAAGCAATTTCAGCTGATCATACAAGTCAAACAGACCTACGCACTTCAATTTTCAATCTCACAAACAAATGAAGTTGACTGCGAAACTACGATCATTATGGAAACATGAACTAACCAAAAGCACTTTTAGAACGTCAAGGCAATGGGTCACTATGTATTGAGAATTGCTATGTTTACTTCATATATCTGTACATCTTGAATTTGCAAATGACATCAATGACTGCTTTGTAGCAGGCTTCCCCATAGTGCTAAAGAGAAGAAAATCATACCATGGTATGATTTAGAGTTTTCTATACAAATGAAAAAACCATTCATTCAATAATTTATCAGAAACTTCACAACACCATTTTCTATGCTTCCATTGTTTATTTAAAATCAGAAGTAGGTATGTAAGTGTAGGTCAGTGTTTGACTCTAGTGTTACTTGAGTTAAGCATTTGACCATTACTTACAGAGGGTCAAAATTACTGAACCAATTTAGACAGGAATGGCTTCTTAGCGAGCCACCTTCATAGCAAGCACTTTCATTTCAGTCAAACCCAAAGTTGTCGCTTGGTCAAACTTTCCACTAAAACCAATGGAAACACTTGCTATGTAGACTATTCTTAGTGTGATATACATTCCTGtagccaccaagacaaagttttgAGAAATTAAGCTAATTGTGATGCAAAATTTGCTGTCTGGACACAAATGCTCAAAGCATTTCATTGACTTGCTAATAGGCTTAGTGGGTATTCTGAGACTGTCATGGTGGCTACAACAGAGTGAGTGACACTGCAAACAGTCGTAGGAATGGCAAGGCCATAGCTAGAAAACACTGTTTCTTTAGTTGACTTGTGGTCAAGCACTATTTTTTCATGTCTTGTAAATTCCTACTGAACTATGGGGGCagctgccccccccccctggtcCTGTGCTAGCTATGGCCCCGCCCCTGTGCTAGCTATGGCCCCGTCCCTGTGCTAAGCTATGGCATGGATAAAACACATGtacttaaaataaaaataaatgttctCTGTACCATCCGTGGTATTGTTGGCTGCATCAACTGCAGGgatcaaataaaaaagaatttaaAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9CXE6	DNA repair protein XRCC3 OS=Mus musculus OX=10090 GN=Xrcc3 PE=2 SV=1
Q08DH8	DNA repair protein XRCC3 OS=Bos taurus OX=9913 GN=XRCC3 PE=2 SV=1
O43542	DNA repair protein XRCC3 OS=Homo sapiens OX=9606 GN=XRCC3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007460 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08423 all species →	Rad51	Rad51	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016467 all species →	Family	DNA recombination and repair protein, RecA-like	Interproscan
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
IPR047348 all species →	Domain	DNA repair protein XRCC3-like, C-terminal	Interproscan
IPR020588 all species →	Domain	DNA recombination and repair protein RecA-like, ATP-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46487 all species →	DNA REPAIR PROTEIN XRCC3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000400 all species →	Molecular Function	four-way junction DNA binding	Interproscan
GO:0000722 all species →	Biological Process	telomere maintenance via recombination	Interproscan
GO:0005657 all species →	Cellular Component	replication fork	Interproscan
GO:0033065 all species →	Cellular Component	Rad51C-XRCC3 complex	Interproscan
GO:0045003 all species →	Biological Process	double-strand break repair via synthesis-dependent strand annealing	Interproscan
GO:0071140 all species →	Biological Process	resolution of mitotic recombination intermediates	Interproscan
GO:0090656 all species →	Biological Process	t-circle formation	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP 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
K10880	XRCC3; DNA-repair protein XRCC3	-	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_048586397.1 across 48 RNA-seq samples of Nematostella vectensis. 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.

48Samples

35TPM > 0

16Conditions

3.0Max TPM

1.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	1	0.98	2.95
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	1.66	2.14
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	1.03	1.14
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	0.93	0.99
whole 6 week old aboral regenerate · regenerate uncut	3	3	1.07	1.11
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	0.33	0.98
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	1.59	2.55
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	1.41	2.05
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	0.77	1.53
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	0.48	0.74
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	0.92	1.18
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	1.85	3.02
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	2.61	2.79
whole 6 week old aboral regenerate · regenerate 48hpa	3	1	0.89	2.67
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	0.67	1.01
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	0.31	0.94

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	2.95
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	2.14
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	1.60
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	1.23
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	1.14
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	1.01
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	0.95
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.99
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.95
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.84
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	1.11
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	1.08
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	1.01
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.98
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	2.55
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	2.22
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	2.05
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	1.86
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	0.31
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	1.53
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.78
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.74
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.69
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	1.18
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	1.00
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	0.57
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	3.02
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	2.53
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	2.79
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	2.78
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	2.26
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	2.67
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	1.01
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	1.00
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.94
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00

Source: CnidoSite RNA-seq expression matrices (NVECT_TPM, StringTie quantification over 48 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 Nematostella vectensis 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	26	XP_048578109.1	0.961108309732369
Negatively correlated	3	XP_001629182.1	-0.53864518230638

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 Nematostella vectensis, 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
NVECT_2month	2 month animal · Adult tissues/organs	1,614	23	not in this dataset	–
NVECT_bodywall	body wall with mesenteries · 6-8 weeks adults	11,742	13	not in this dataset	–
NVECT_embryo	embryos · 8, 10 and 12 h after fertilisation (deposit labels 8h/10h/12h)	9,711	17	not in this dataset	–
NVECT_gastrula	Blastula-gastrula intermediate · Developmental stages	49,166	27	not in this dataset	–
NVECT_gastruloid	dissociated and reaggregated embryos · 4-48 hpa	36,550	8	not in this dataset	–
NVECT_neoplasm	neoplasm · Adult tissues/organs	2,532	16	not in this dataset	–
NVECT_nervous	Gastrula Cells · nervous system	16,590	27	unmapped	–
NVECT_notch48h	embryos treated 24-48 hpf (DMSO vs LY411575) · 48 hpf	19,044	7	not in this dataset	–
NVECT_tentacle	tentacle · Adult tissues/organs	7,977	19	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_gastrulae_24h	1	Promoter (<=1kb) 1
	H3K27ac_planulae_4days	1	Promoter (<=1kb) 1
	H3K4me2_gastrulae_24h	3	Promoter (<=1kb) 3
	H3K4me2_planulae_4days	1	Promoter (<=1kb) 1
	H3K4me2_polyps	1	Promoter (<=1kb) 1
	H3K4me3_gastrulae_24h	1	Promoter (<=1kb) 1
	H3K4me3_planulae_4days	1	Promoter (<=1kb) 1
	H3K4me3_polyps	1	Promoter (<=1kb) 1
	H3K36me3_gastrulae_24h	1	Promoter (2-3kb) 1
	H3K36me3_planulae_4days	6	Exon 4 · Promoter (2-3kb) 1 · 3' UTR 1
	H3K36me3_polyps	4	Exon 4
	H3K4me1_gastrulae_24h	2	Promoter (1-2kb) 1 · Promoter (<=1kb) 1
	H3K4me1_planulae_4days	3	Promoter (<=1kb) 3
	H3K4me2_neuronal_ELAV_cells	1	Promoter (<=1kb) 1
	late_gastrula	1	Promoter (<=1kb) 1

1 further sample(s) also have peaks at this gene; open the assay page below to see them all.

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

DNA methylation (bisulphite samples)

Sample	Methylation profile
Whole_adults	open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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 →