Gene detail

Detailed information of Ppa0G326050 in Paragorgia papillata

Genomic Location: Contig00473:111755...135173
NR annotation: XP_028394772.1, DNA repair protein RAD50-like [Dendronephthya gigantea]
Species Paragorgia papillata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Ppa0G326050

ATGTCTCAAATTGAGAAACTACAGATTGATGGGATACGAAGTTATGGTCAACCAGCAGTCATTGAATTTTTTACTCCTCTGACTTTAATTATTGGAGCAAATGGAGCTGGCAAAACGACAATTGTTGAGGCACTTAACTACATTACAACTGGAGATATGCCACCAGGCAGCAAAGGAGCTGCTTTTGTTTACGACCCAAAGATTGCTGGTGAACAAGAAGTCAAAGGTCAAGTGAAACTGATGTTAAAGGATTACATGGGTCAACGTGTTATTGCAACTCGATCTTTACTTTCAACCCAAAAGACAAAGAAGATTGAATGCAAATCAATTGAGAATGTAGTTAAAAGACAAAAAAATCACGAGTGGGTCAGTGTAAGCTCCAAATGTGGTGATATTAACAGAGAAATGATAGCATGTCTTGGAGTTTCAAAACCTGTCTTGGACTGTGTGATATTTTGTCATCAAGACGATTCATTGTGGCCACTGAGTGAAGGGAAAGTGTTGAAATCGAAATTTGATGACATTTTTGCTGCGACAAGGTATATAAAGGCTCTAGAGGAAATACGGAAGTGTAAAGTGGAGTTAGACTATTTGCAAGCTCATAAGGACAAGACAGTTCAGATTGAAGAAACTTTGGAAAACACTTTACAGAAGCACAATGAAACGCAAGTTCAGGTTGAAGACTTAAAAAAGTCGATGAAACCAGTGGAATCCCGCTTGAGAGAGCTGGCGCAAATCCAAAACGATCTCATTGAGTTAGAGAAGAACTTGGAGATATTCAATTCAGAGAAAAAAAATCTTATGGCAACTAATGAAAAGTTAAACAGCAATATAACTAACTTGTTTGAAGGAGATCAGGAAGAGCTGGAGAAATTTTACAATGGGTATGAATCAAAAGTTGTTGAAAAGGAGAAACAGTTACAGGAAATCGAAGAACGCGTTAGAGGAAAAGGTCGAGAACACACAAGATTGAATTCCGAGAAGAGCGCCATTTTAATTAGACACGGCAAGTTGCAGCAAGAGGCGGAGCGTCACAAATCAGACATAAAGGAAAGAGATTCCATGATCGTTGATCAGTCTAAGATACTTCATTTTAAAGGTTTTGAGAATCCCCCTTTTTCTCAGGAGAAGGTCACTAGTTTTGTGGACTCAAGGAAAGAGAGATACCAGAATTTGGTGCAGGAGAGAAACGACTCTAAACAAGCTTTTCAAGAACGAATCGACTCCATTCAAGAAAAGATTGATGGTATTAAGAAAACTCTTTATCAATACGAAGAAACAATCAGAATTAAAAACAACTTGTGTGCAGAGAATCAGAAGAAGTTGAAACAAATTGCTCGTGATCTTAGTAACGTAGACGTTTCTCAAAAAAAGCTCCAGCGAATCGAGAAAGATTTGAAAACAGCGGAAAAAGAGCTCGAAGATACTAAGGCAAGTGGAAACGTCGGGCAGTGGAGAACCGAACTTGAGGAATCACAAAAGGAGAAGCGCCGACTGGAGTCCGATTTGAATCGACTACGAGACGAACAACATACAATGACCCTCCAGTCGACGACCCAAGCAAAACTGGACATGTCTAGGAAACAAAGAGAGGCCAAGGAAGACGCTATCCAGAAAATTCTGGACCGACATGAGGGAGAATTACAAATCATGTTTGGAGCTTGTGGTCCTATAGACACAGTAAAGACACGAGTTTCGAAATTTCTTCAAGAGAAACGTTCAGAATTAAATAACATGGACAGTAACATCCAGAAATTGAAACAACAACAATCGTCAAAACAAGCCGAAAAAAGAATGATCGTAGACGAGATTGCGAATCTTGAAAAGCTCATGTCTGAATACAAGGATAAAATAAAGCAAGCTTGTGGTGAAAAAGAGTACTCGTTATTGAAAAACGAGGTTTATGACGCCATTGAACAAGCAAAGAGTAAGTGCAGTCAGTTATCAGCTTTCGAAACGATTTATAAAAAGTATATCTCGAATATGGAAGCGAAAGAGAAGGCGGAGTCTTGTTGTCCTCTATGTCACAGACAGTTTGGTGATTTGAAAGAGATGCAGAATCTTGTGGACGAGCTTAAAGATAAGATTCGTAGAGTACCTGAGAAAGTGCGCTCACAGAAAGAGAACCTTCAACGGGACGAAGAGATCCATGGCCGATTGCAGAAATTGACCTCTGTTAAAGACAATTTGGAAGACATTGAAAACAAAAAGTTGCCCAATGCCAAGCAAAAATTGTCAAACATATTGCTGGAACTTGTGAAACTACAAAGCAAAATCGAAGAGATGGAAGATGTTCGTAGTGTAGTCGAGAGTGAAGAAATTGCAGCACGGCAGATGGAACCTGATTTTATCATGTTGGAGGAACATCAGAAGTCGTTGAAAATTTTAGACAAGGAGATTAGTCTTCAGCAGGCTAAAATTGAAGGCGTTGCTCCAGGTCGCAGTATGCAGTTGGTTAACAATGAGATATCAGACTGCCAGGATCGCGTCGACGGTCTTAATCGTGTTATTGATCGTAAAAGAAACCAAATATCTCAACTGGAGAGCCAAATTTCTTCGTCCATGGCAAGTGTTCACGAGTTGAGTTCGGAGAAGATGCGGTTGAGCGGTGAACTTCAGAAAAGAACACGTCTAGAAGAACAAAAAGCTGAGCTGACTGCAGCGAATATGGAACATGAGAGAGACGTTAAGGAAGCAGAAAGGCAACTACAACCCATTAAGAAAAGTCTGAAAGAACTGGAGCAACAGCACAAGTCGCTTGTCGTAGAACAAGAAGCAGTTGTTGCGAAAACAAATACCAAGTTGAATGATATTAAAGGTCACGCCACGAAACTTAAGGACAAGATGACAGAAATTCGCAAATACGAGAACGACAATCGCGAAAGCGTTCTACAAGAAGTCAAAGGAAACTTAGCTACCATAGAGGACCAGATAAAAAGAATAAGCAACGAGAGTGGAAGATTTTCTTCCCAAATGGATGAATTAAAAGACGATTTATCTCGCACGAAGGTTCGTGTACGTGAACTCCAAGATAACATTCAGCTACTTGAGAATGCAGCGAAGATTTCTAAACTGGAGAGAAGGATTGTTCGTGTGAAAAAGGAGGAAGAGAAGCTTGGCAACTATGATGAAGTGATGAGAGAGAAAGATGTTCTAGAGAAACGGTTGGGAGACTGCCGTAAACAGAAAGCTACTTTCGAAGGACGTCAAACTGGTTACGAGGAAGAAATTACGAGATTTCAAAAAGAACTTCAAAGTTCCTTATATAAAGATGCAGGGGAAAAACATCGCGAGAAACTTATTGAAATTACGACGACGGAACTTGCAAACAATGATCTGGAGAAATACGGCAAAGCTTTAGACAGAGCAATCATGAAATTTCACAGCATAAAAATGGAAGAGATTAACAAGGTTGTGAAGGAGTATTGGATAAACACGTACAAAGGAAATGATATTGACACAATTGAGATTCGTTCAGATGACGACACTGACGGAGCGTCCATTTCTGCTCGCAGAAGTTACAACTACAAAGTTGTAATGATAAAAGGAGACGTAGCGTTGGACATGCGTGGTCGGTGTAGTGCAGCGTTAGCTGAATCGTTTTGCTTGAACTGTGGAATCCTCGCTCTTGATGAACCGACCACAAACCTGGACGAAGAGAATATTGCAAGCTTGGCCAATCAACTAGCCACCATTATAAATTCCCGAAGTCCGCAGAAGAACTTCCAGTTGGTTGTTATCACGCATGACGAACATTTTGTTGAACTTCTTGGCCAGGCAGATTTTGTGGAATATTATTATCGCGTTGCAAAAGATGAAGAAGGTATTTCCAGAATCTATAAACAATCTACTTCAGGAGAGGAGACAGTGTGA

Transcript

Ppa0G326050

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9JIL8	DNA repair protein RAD50 OS=Rattus norvegicus OX=10116 GN=Rad50 PE=1 SV=1
A0A1L8GXM0	DNA repair protein RAD50.L OS=Xenopus laevis OX=8355 GN=rad50.L PE=1 SV=1
Q92878	DNA repair protein RAD50 OS=Homo sapiens OX=9606 GN=RAD50 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001873 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04423 all species →	Rad50_zn_hook	Rad50 zinc hook motif	Motif	Interproscan
PF13476 all species →	AAA_23	AAA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013134 all species →	Domain	RAD50, zinc hook	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR004584 all species →	Family	DNA repair protein Rad50, eukaryotes	Interproscan
IPR038729 all species →	Domain	Rad50/SbcC-type AAA domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR18867 all species →	RAD50	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000723 all species →	Biological Process	telomere maintenance	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0030870 all species →	Cellular Component	Mre11 complex	Interproscan
GO:0000722 all species →	Biological Process	telomere maintenance via recombination	Interproscan
GO:0000794 all species →	Cellular Component	condensed nuclear chromosome	Interproscan
GO:0003691 all species →	Molecular Function	double-stranded telomeric DNA binding	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0007004 all species →	Biological Process	telomere maintenance via telomerase	Interproscan
GO:0032508 all species →	Biological Process	DNA duplex unwinding	Interproscan
GO:0043047 all species →	Molecular Function	single-stranded telomeric DNA binding	Interproscan
GO:0051880 all species →	Molecular Function	G-quadruplex DNA binding	Interproscan
GO:0070192 all species →	Biological Process	chromosome organization involved in meiotic cell cycle	Interproscan
GO:0090305 all species →	Biological Process	obsolete nucleic acid phosphodiester bond hydrolysis	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
K10866	RAD50; DNA repair protein RAD50	EC:3.6.-.-	DNA repair and recombination proteins	ko03400	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Paragorgia papillata 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Paragorgia papillata, 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.	no expression matrix	–
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 →