Gene detail

Detailed information of RMX51955.1 in Pocillopora damicornis

Genomic Location: SczhEnG_1707:653888...668419
NR annotation: no NCBI-NR hit recorded
Species Pocillopora damicornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

pdam_00004771

ATGAGCACTGTAGACTCCTACGGGCCTGCATCTCAAACTTTGACTTTTTTAGACACTGAAGAAGCTGATTTCGGTGCGGACACACAAGGAAGCGAGTACGAATTTCACGACTTTACAGTACCTTCGCAAACCCAAACCCAATCTCAAGCTTCACAACCTGAACCGAGCCAACCTTTGGTCAATGGCAACGTCGCAGACAAAAAAGAAGATCTAGCTAACGGCCCAACAACAGGAAACGAAGAAGCTAAGGTGGATGGTACCGTTTCTAAGGTTAGCAACTCTTTGGGGGAGCTTAACTTTGAAGAAGATGAGGACGAGACTTTTTACTCGAAGGATCTTCCAGCCTTCGCTTGCAGGTATTGTGGAGTTCATGACCCAGCATCTGTTGTGCAGTGCATTCAGTGCAAGAAGTGGTTCTGTAATGGGCGAGGAAACACTGCAGGCAGTCATATTGTAAACCACCTTGTAAGAGCCAAGCACAAAGAGGTTACACTTCACAAAGATGGTCCTTTGGGGGAGACAATCTTGGAATGCTACAACTGTGGCTGCCGCAATGTCTTCTTGTTGGGATTTATTCCTGCCAAGGCTGATTCAGTTGTGGTGTTACTGTGCAGACAACCCTGTGCTACACAGAGTAACTCCAAGGACATGAACTGGGACCAGGCACAGTGGCAGCCTCTGATTAATGATAGGTGCTTCTTGTCCTGGCTTGTTAAAGTTCCACCTGATGAGGATCAGCTGCGAGCCAGACAGATCTCTGCACAACAGATTAACAAGCTCGAAGAACTGTGGAAGGATAATCCTGAAGCTAAGTTAGAAGATTTGGATAAACCAGGAGTTGATGATGAACCACAACAAGTTCTTCTCAGGTATGAGGATGCCTACCAATATCAAAACATCTTTGGCCCACTGGTTAAACTGGAAGCAGATTATGACAAGAAGCTGAAAGAGTCTCAGACTCAAGATAACATTGTTGTTCGTTGGGACATTGGTCTCAACAAGAAAAGGATTGCATACTTCTCCTTTCCCAAGACAAATGATGACATGAGATTGATGCCTGGTGATGAACTCCGCCTGCGATATGTTGGGGAATTACACAAACCTTGGCAGGGTGTTGGTCATGTGATCAAAGTGCCGAACAACTTTGGTGAGGAAGTGGGGATTGAGTTGCGCAGCAATCTGGGTGCCCCAGTTGAATGTACTCATAACTTTGTTGTGGACTTTGTGTGGAAATCAACCTCATTTGACAGAATGCAAACAGGAATGAAGACCTTTGCTGTGGATGAAACATCAGTCAGTGGCTACATCTACCACAAGCTGCTGGGTCATGAGGTGGAAGAACAGGTTGTCAAATGCCAGCTGCCTAAGAGGTTTTCAGCCCAAGGTCTGCCAGAACTGAACCATTCACAAGTGTATGCTGTCAAGACTGTCTTACAAAGACCACTTAGTCTTATCCAGGGACCCCCGGGTACCGGAAAAACAGTCACATCAGCCAGTGTTGTTTATCACCTAGCCAAGCAAAACAATGGTCAAGTTCTTGTCTGTGCTCCAAGTAACATTGCAGTGGACCAGTTGACAGAGAAAATCCACAAGACAGGACTCAAGGTTGTGAGACTGTGTGCCAAGAGTAGAGAGGCTATTGACTCTCCTGTGGCATTCCTTGCACTGCACAATCAAGTGCGTAACATGGACAGTGTTCCTGAACTCCAAAAGCTGCAGCAGCTCAAAGATGAGCAGGGTGAGCTGTCTGCCGCTGATGAGAAGAGGTACCGATCTCTGAAGAGAAATTGTGAACGTGAGCTTCTCCAGCATGCAGATGTGATTTGTACCACTTGTGTTGGTGCTGGTGACCCTCGCCTGTCCAAGTTCAGATTCCGTACTGTGCTGATTGATGAGTCAACCCAGGCCACTGAACCAGAGTGTATGGTGCCTGTTGTTCTTGGCTGCAAACAGCTCATCCTTGTTGGTGATCATTGTCAGCTTGGTCCTGTTGTGATGTGCAAGAAAGCAGCAAATGCTGGTCTGTCTCAGTCTTTGTTTGAACGTCTGGTGGTTCTTGGGATCCGTCCTATTCGTCTCCAAGTCCAGTATCGTATGCACCCTTCCCTGAGCGAGTTCCCATCCAATCTGTTTTATGACGGAACTCTTCAGAATGGAGTCACTGTTGCTGAACGCCAGCAGACCGGGATTGACTTCCCTTGGCCTGTTCCCGATAAGCCAATGACTGAAGCTGCAAACGTGGAGAAGATTGCCACTCGATTTCTCCGTGCTGGCGTGAAACCAGAGCAGATTGGAGTGATAACTCCGTATGAGGGTCAGAGAGCTTACATCGTACAGTACATGCAGTTTAGTGGCTCTCTTCATGCCAATCTTTATCTGGAAATCGAGGTAGCCAGTGTCGATGCATTCCAGGGCCGGGAGAAGGACTACATTATCCTGTCCTGTGTACGCTCCAACGAACATCAGGGAATTGGTTTCTTGAATGATCCGAGACGTCTGAACGTGGCTTTGACCCGAGCAAAATATGGAATCATTGTCATTGGCAACCCCAAGATCCTATCCAGGCAACCTCTGTGGAACCATCTGTTGAATTACTACAAAGAAAATAAGGCTTTGATGGAAGGACCCCTGAACAATTTAAAGGAAAGCATGATTCAGTTTAGCAAGCCAAGGAAACTTGTTAACCGTACAAATCCGGGTGGCCGTTTCATGAGCAGCACGATGTTCGACGCCCGTGAAGCGCTGATCCGCGGTAGTGTGTATGACCGTCAGATACCTCAGGCACCCATGGATCCTGCAGCCTTCCATGACACTTACTTCCACACGCATGACCGGCTCAGTTACATCGGAGCCGAGCGAACCATTCCACCCGCTGCTGCAGCAAGGATCCCGGTACCCGTGGGGATGTTTATTCCTCCGGTGCCTCCCCCACACCACTCCTACTTTGGGCAGCCTCTTGCCGGTCGAATGCCTCATGGCCGACCAGTTCAGCAGCCTCGGCAGCGAAATCAGCGCAACCATCATCACCAGCAACCAATGGCGTATGCTCCTCACATGCCAGCCAGCCAGGCCAGTCAGGATGCTTCCCAGCCTCTGTCCCAGGGCCCACTCACTCAGGGTGGCATGTCCATGAGTCAGCCCATGGCCTCACAGCCATTGTCGCAGCCGGACCTATCTCAGGATAGTTACCTTGGAGACGACTTCAACCTGAAATCCCAGGCAGATGCTGTGTTGTCACAGGATTCTACCTACCAAGGGGAGAGGGGAGGCTACATGAACTCCTTACCAGACTACTCCCAACCAAACTATGCCTCTCAGTACTGA

Transcript

rna-pdam_00004771

GTGGCTGAAGTCGCCATCTTGGCCACGTTCTTACGATAGATTTCAAAATCCTCCGATACTTTCGTTTTAACTGTCGTAACTGAGacagtttttactttttttcgtCTGAAAGATGAGCACTGTAGACTCCTACGGGCCTGCATCTCAAACTTTGACTTTTTTAGACACTGAAGAAGCTGATTTCGGTGCGGACACACAAGGAAGCGAGTACGAATTTCACGACTTTACAGTACCTTCGCAAACCCAAACCCAATCTCAAGCTTCACAACCTGAACCGAGCCAACCTTTGGTCAATGGCAACGTCGCAGACAAAAAAGAAGATCTAGCTAACGGCCCAACAACAGGAAACGAAGAAGCTAAGGTGGATGGTACCGTTTCTAAGGTTAGCAACTCTTTGGGGGAGCTTAACTTTGAAGAAGATGAGGACGAGACTTTTTACTCGAAGGATCTTCCAGCCTTCGCTTGCAGGTATTGTGGAGTTCATGACCCAGCATCTGTTGTGCAGTGCATTCAGTGCAAGAAGTGGTTCTGTAATGGGCGAGGAAACACTGCAGGCAGTCATATTGTAAACCACCTTGTAAGAGCCAAGCACAAAGAGGTTACACTTCACAAAGATGGTCCTTTGGGGGAGACAATCTTGGAATGCTACAACTGTGGCTGCCGCAATGTCTTCTTGTTGGGATTTATTCCTGCCAAGGCTGATTCAGTTGTGGTGTTACTGTGCAGACAACCCTGTGCTACACAGAGTAACTCCAAGGACATGAACTGGGACCAGGCACAGTGGCAGCCTCTGATTAATGATAGGTGCTTCTTGTCCTGGCTTGTTAAAGTTCCACCTGATGAGGATCAGCTGCGAGCCAGACAGATCTCTGCACAACAGATTAACAAGCTCGAAGAACTGTGGAAGGATAATCCTGAAGCTAAGTTAGAAGATTTGGATAAACCAGGAGTTGATGATGAACCACAACAAGTTCTTCTCAGGTATGAGGATGCCTACCAATATCAAAACATCTTTGGCCCACTGGTTAAACTGGAAGCAGATTATGACAAGAAGCTGAAAGAGTCTCAGACTCAAGATAACATTGTTGTTCGTTGGGACATTGGTCTCAACAAGAAAAGGATTGCATACTTCTCCTTTCCCAAGACAAATGATGACATGAGATTGATGCCTGGTGATGAACTCCGCCTGCGATATGTTGGGGAATTACACAAACCTTGGCAGGGTGTTGGTCATGTGATCAAAGTGCCGAACAACTTTGGTGAGGAAGTGGGGATTGAGTTGCGCAGCAATCTGGGTGCCCCAGTTGAATGTACTCATAACTTTGTTGTGGACTTTGTGTGGAAATCAACCTCATTTGACAGAATGCAAACAGGAATGAAGACCTTTGCTGTGGATGAAACATCAGTCAGTGGCTACATCTACCACAAGCTGCTGGGTCATGAGGTGGAAGAACAGGTTGTCAAATGCCAGCTGCCTAAGAGGTTTTCAGCCCAAGGTCTGCCAGAACTGAACCATTCACAAGTGTATGCTGTCAAGACTGTCTTACAAAGACCACTTAGTCTTATCCAGGGACCCCCGGGTACCGGAAAAACAGTCACATCAGCCAGTGTTGTTTATCACCTAGCCAAGCAAAACAATGGtCAAGTTCTTGTCTGTGCTCCAAGTAACATTGCAGTGGACCAGTTGACAGAGAAAATCCACAAGACAGGACTCAAGGTTGTGAGACTGTGTGCCAAGAGTAGAGAGGCTATTGACTCTCCTGTGGCATTCCTTGCACTGCACAATCAAGTGCGTAACATGGACAGTGTTCCTGAACTCCAAAAGCTGCAGCAGCTCAAAGATGAGCAGGGTGAGCTGTCTGCCGCTGATGAGAAGAGGTACCGATCTCTGAAGAGAAATTGTGAACGTGAGCTTCTCCAGCATGCAGATGTGATTTGTACCACTTGTGTTGGTGCTGGTGACCCTCGCCTGTCCAAGTTCAGATTCCGTACTGTGCTGATTGATGAGTCAACCCAGGCCACTGAACCAGAGTGTATGGTGCCTGTTGTTCTTGGCTGCAAACAGCTCATccttgttggtgatcattgtCAGCTTGGTCCTGTTGTGATGTGCAAGAAAGCAGCAAATGCTGGTCTGTCTCAGTCTTTGTTTGAACGTCTGGTGGTTCTTGGGATCCGTCCTATTCGTCTCCAAGTCCAGTATCGTATGCACCCTTCCCTGAGCGAGTTCCCATCCAATCTGTTTTATGACGGAACTCTTCAGAATGGAGTCACTGTTGCTGAACGCCAGCAGACCGGGATTGACTTCCCTTGGCCTGTTCCCGATAAGCCAATGACTGAAGCTGCAAACGTGGAGAAGATTGCCACTCGATTTCTCCGTGCTGGCGTGAAACCAGAGCAGATTGGAGTGATAACTCCGTATGAGGGTCAGAGAGCTTACATCGTACAGTACATGCAGTTTAGTGGCTCTCTTCATGCCAATCTTTATCTGGAAATCGAGGTAGCCAGTGTCGATGCATTCCAGGGCCGGGAGAAGGACTACATTATCCTGTCCTGTGTACGCTCCAACGAACATCAGGGAATTGGTTTCTTGAATGATCCGAGACGTCTGAACGTGGCTTTGACCCGAGCAAAATATGGAATCATTGTCATTGGCAACCCCAAGATCCTATCCAGGcaACCTCTGTGGAACCATCTGTTGAATtactacaaagaaaataaggcTTTGATGGAAGGACCCCTGAACAATTTAAAGGAAAGCATGATTCAGTTTAGCAAGCCAAGGAAACTTGTTAACCGTACAAATCCGGGTGGCCGTTTCATGAGCAGCACGATGTTCGACGCCCGTGAAGCGCTGATCCGCGGTAGTGTGTATGACCGTCAGATACCTCAGGCACCCATGGATCCTGCAGCCTTCCATGACACTTACTTCCACACGCATGACCGGCTCAGTTACATCGGAGCCGAGCGAACCATTCCACCCGCTGCTGCAGCAAGGATCCCGGTACCCGTGGGGATGTTTATTCCTCCGGTGCCTCCCCCACACCACTCCTACTTTGGGCAGCCTCTTGCCGGTCGAATGCCTCATGGCCGACCAGTTCAGCAGCCTCGGCAGCGAAATCAGCGCAACCATCATCACCAGCAACCAATGGCGTATGCTCCTCACATGCCAGCCAGCCAGGCCAGTCAGGATGCTTCCCAGCCTCTGTCCCAGGGCCCACTCACTCAGGGTGGCATGTCCATGAGTCAGCCCATGGCCTCACAGCCATTGTCGCAGCCGGACCTATCTCAGGATAGTTACCTTGGAGACGACTTCAACCTGAAATCCCAGGCAGATGCTGTGTTGTCACAGGATTCTACCTACCAAGGGGAGAGGGGAGGCTACATGAACTCCTTACCAGACTACTCCCAACCAAACTATGCCTCTCAGTACTGAAGTACTAGCCTACCGGCTGTGAAGGGGGCACGTCGTCACCTGGCAGCCGTCGTCAAGGCAACCAGAAGGTAACACCTTGCTTAAGCCACACCCTTGATTGTCCCCACACTGAGGGTGTGGTGCTGACTAAaaccttgaagaaaaaagagaggagAGAGTGGAACGAGaagagaggagaaaaatttcaccCGCATTTACAAACGACGGGTCTCAACGGTTTTGACGCCgcgaacagaaaaaaaatgaagttttttttttggaactttGACTTGGTGGTTTTTAGACGGTTCTTGACCTGACGAGCAAAGCTTCGCTAGTTttatagaagaaaaaagacattgGTAGGGTGCCGTGAAACGACAAGAAAGAACCAGCTTTATAATTTACCTCGACGTGATTGTGGACAGTTGGTCGTAACACAGCAGACAGCCCAGatctttcacttttcttgAGCTCCCTGTCACACAGTAGACCCCACAGCTAGCTTGCTTACTATTGACGTTTCTTTCATCACTGATATTCACAAAAGCAAGACGAACTTGCTTCCAAATAATTAAATGCAAGATCTTGGTAAAGATTAACAGATTCTCCTATGAAGTTTTTGTTATGGATTTTTATCGGAAATCTCTTTCCCCAATTTGAAACTAAACATTCCAAGCAAGACATCTGTAACAAAGGTTGTGGACGAACTGTTTGAGTTCTACAACGTGATGTCCACTTTATCTTCGAAGTGAGACGTTTCGTAAACTTAAACCTCGGTTACgagaaaaatcagtttaatgTTGCTTGGTTGATAAGCCTCATCTTATTTAAACTTACTGCAAAGACCTTTCCTTTAATGACTATTTGCTTTAGTTCTAGTGACTAAACTATGGTTACGTTAGAACTTCCAACCTCTTTTAGCTTCTAAAATAAGCGCAAGACATTCCTTAAAGCTGCCGCTGGTTTTAGAGGACAGAACTGAGGACAAAACAGACGTGTTTTGGATAGAATGTTGCCCATAAATTTGTCTCTGTCTCCAAAAGGGAACAAGTTTTTAAGAAGTCAGGAAACGATGGGTGTGCGTCCcgtgaagtttttttttgaagcaGGGTGTACGGAAGTGCATCTTGTTTCgtatttgttgttattttgttgtaagCTTTTGAATAATGTTAGAGTTATTGGTGTTTTCATTGATCCTATAATCCACTTCCTAGTTCAATCCGTGGTTGATGTTCTCTTAGGGCTAAGTGTGTGATacattattacttttatttttagtacTGTTATTACAAACCTTTTTGGCAGATGCGTTTGATGTGAGTTCAAAGTTGTAGTGCATTCTCTTGTGAGtgattgaaggaaatttttgtaatttagtCAGGTCGTGAAGTTAGCTTTGGTGTTTTCGCACTCATGATAATAGGAacattctttgtttcaaaatata

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004432 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09416 all species →	UPF1_Zn_bind	RNA helicase (UPF2 interacting domain)	Domain	Interproscan
PF18141 all species →	UPF1_1B_dom	RNA helicase UPF1, 1B domain	Domain	Interproscan
PF13086 all species →	AAA_11	AAA domain	Domain	Interproscan
PF04851 all species →	ResIII	Type III restriction enzyme, res subunit	Family	Interproscan
PF13087 all species →	AAA_12	AAA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018999 all species →	Domain	RNA helicase UPF1, Cys/His rich zinc-binding domain	Interproscan
IPR040812 all species →	Domain	RNA helicase UPF1, 1B domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR047187 all species →	Domain	Upf1-like, C-terminal helicase domain	Interproscan
IPR041677 all species →	Domain	DNA2/NAM7 helicase, helicase domain	Interproscan
IPR006935 all species →	Domain	Helicase/UvrB, N-terminal	Interproscan
IPR041679 all species →	Domain	DNA2/NAM7 helicase-like, C-terminal	Interproscan
IPR045055 all species →	Family	DNA2/NAM7-like helicase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10887 all species →	DNA2/NAM7 HELICASE FAMILY	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0004386 all species →	Molecular Function	helicase activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase 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
K14326	UPF1, RENT1; regulator of nonsense transcripts 1	EC:5.6.2.5 EC:5.6.2.3	Messenger RNA biogenesis	ko03019	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 Pocillopora damicornis 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 Pocillopora damicornis, 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 →