Gene detail

Detailed information of evm.model.Ap1.546 in Astrangia poculata

Genomic Location: Ap1:5032485...5049421
NR annotation: XP_020609660.1, regulator of nonsense transcripts 1-like [Orbicella faveolata]
Species abbreviation APOCU · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.Ap1.546

atgagcactgtagactcttacggacctgcgtctcaaacattgacctttttagacaccgaagaagcagatttcggcgcagatacacaaggaagcgagtacgaatttcacgattttactgtaccatcgcaaactcaaacccagtcgcaagcttcgcaacctgaagcgagccaacctttggttaatggaagtgctgtggacaaaaaggaagagctgactaatggcccagtagcggtaaacgaagattctaaagcagatggcagcgtctccaaggttagcaactctttgggagagcttaacttcgaagaagatgacgacgaaaccttttactcgaaagatcttccagcctacgcatgcaggtattgtagagtccatgacccagcttctgttgtccagtgcattcagtgcaagaagtggttctgtaatggacgtggaaacacggctggcagccatattgtgaaccatcttgttagagccaagcacaaggaagtgacacttcacaaggatggtcctttgggcgagacaatcttagaatgctacaactgtgcttgtcgcaatgtgttcctgttgggtttcatcccagccaaggcagattcagttgtggttttactgtgtaggcaaccttgtgcaacacagagtaactccaaagatatgaactgggatcaagcccaatggcagcctctgattaatgaccgctgcttcctgtcatggcttgtcaaagttccgcctgatgaggaccaactgagagcaagacagatctcagcccagcagattaacaagcttgaagaactgtggaaggataaccctgaagctaagttagaagatctggataagcctggagtagatgatgaaccacaacaagttcttctcaggtacgaggatgcttaccagtatcagaacatatttggcccacttgtaaaactggaagcagattatgacaagaagctcaaggaatctcagactcaagataacattgttgttcgttgggacattggtctaaacaagaaaaggattgcatatttctcctttccaaaaacaaatgatgacatgcgactgatgcctggtgatgagctgcgactgagatatgttggtgaattgcacaaaccctggcagggtgttggtcatgtcaccaaagtgccaaacaactttggagaggaagttggaattgagttgcgcagcaatctaggagctccagtagagtgcactcataattttgtggtggactttgtgtggaaatcaacttcttttgatagaatgcagacaggaatgaagacctttgcagttgacgagacatctgtcagtggttatatctatcacaagctgctgggacatgaggtggaggaacaggttgtcaaatgccagttgcctaaaaggttttcagcccaaggtctgccagagcttaaccattctcaagtgtatgccgtgaagactgtactgcaaagaccacttagtcttattcagggacccccaggcactggtaagactgtgacatcagctagtgttgtgtatcacctggccaagcaaaacaatggtcaagttcttgtctgtgctccaagtaacattgcagtggatcaactgacagagaagatacacaagacaggactcaaggttgtaagactgtgtgccaagagcagagaggcaattgactctcctgtagccttccttgcactgcacaatcaagtgcgtaacatggacagtgttccagaattgcaaaagctgcagcaactcaaagacgagcagggtgagctgtctgctgctgacgagaagagatacaggtccctgaagaggaactgtgaacgagacctgctgcagcatgcagatgtgatctgtaccacttgtgtgggtgctggtgaccctcgcctgtctaagttcaggttccgtactgtactgatcgatgagtcaacccaagcaactgaaccagagtgcatggtgccagtcatacttggctgcaaacagctaatccttgttggagatcactgtcagctgggtcctgttgtgatgtgcaagaaagcagccaatgctggtctgtctcagtccctgtttgaacgtctggttgttcttggaatccgccccattcgtctgcaagtccagtatcgtatgcaccccgccctgagcgagttcccgtccaatctgttttatgatggaactcttcagaatggagtcactgttgctgaacgtcagcagtctggtattgactttccatggcctgttcctgacaagccaatgttcttctactccaccatgggccaagaggaaattgcctcctctgggacatcctaccttaacagaactgaagctgccaatgtagagaagattgccacccgatttcttcgtgctggagtgaagccagagcagattggagtgatcactccatatgagggtcagagagcttaccttgtacagtacatgcagttcagtggatctcttcatgccaacttgtacctggaaattgaagtggccagcgttgatgcattccaaggacgagagaaagactacattatcctgtcttgtgtccgctccaatgaacatcagggcattggtttcttgaacgatccaagacgtctgaacgtggccttgactcgagcaaagtatggcatcattgtcattggcaatcccaagattttatccaggcaacccctgtggaaccatctgttgaactactacaaagagaacaaagctttgatggaaggacccctgaacaatttgaaagaaagcatgatccagttcagcaagccaaggaaacttgtcaaccgcaccaatccgggcggccgtttcatgagtagcaccatgtttgatgcccgtgaagctctaatccgcggcagtgtgtatgacaggacgatgcctacagcacccatggacccagctgccttccatgacacttacttccacactcatgaccgtctaagctacatcggagctgagcgtaccatcccacctgctgctgccgccaggataccggtacccgtgggaatgttcatcccccctgtacctcccccacaccactcttactttggccagcctcttgccggccgtatgcctcacggtcggccagtccagcagccccggcaacgcaatcagcgaaaccatcaccctcagcagccaatggcttacgcacctcacatgccagccagccaggccagtcaggatgcttcccagccactgtcccagggcccactcactcaaggtggtatgtctatgagtcagcccatggcttcacagcccttatcacagccggacctgtctcaggacagttacttgggagacgatttcaacctcaagtctcaagcagatgcggtgttgtcccaggactccacctaccaaggggagaggggaggttacatgaactccttaccagactactcccagccaaactatgcctcccagtactga

Transcript

evm.model.Ap1.546

ATGAGCACTGTAGACTCTTACGGACCTGCGTCTCAAACATTGACCTTTTTAGACACCGAAGAAGCAGATTTCGGCGCAGATACACAAGGAAGCGAGTACGAATTTCACGATTTTACTGTACCATCGCAAACTCAAACCCAGTCGCAAGCTTCGCAACCTGAAGCGAGCCAACCTTTGGTTAATGGAAGTGCTGTGGACAAAAAGGAAGAGCTGACTAATGGCCCAGTAGCGGTAAACGAAGATTCTAAAGCAGATGGCAGCGTCTCCAAGGTTAGCAACTCTTTGGGAGAGCTTAACTTCGAAGAAGATGACGACGAAACCTTTTACTCGAAAGATCTTCCAGCCTACGCATGCAGGTATTGTAGAGTCCATGACCCAGCTTCTGTTGTCCAGTGCATTCAGTGCAAGAAGTGGTTCTGTAATGGACGTGGAAACACGGCTGGCAGCCATATTGTGAACCATCTTGTTAGAGCCAAGCACAAGGAAGTGACACTTCACAAGGATGGTCCTTTGGGCGAGACAATCTTAGAATGCTACAACTGTGCTTGTCGCAATGTGTTCCTGTTGGGTTTCATCCCAGCCAAGGCAGATTCAGTTGTGGTTTTACTGTGTAGGCAACCTTGTGCAACACAGAGTAACTCCAAAGATATGAACTGGGATCAAGCCCAATGGCAGCCTCTGATTAATGACCGCTGCTTCCTGTCATGGCTTGTCAAAGTTCCGCCTGATGAGGACCAACTGAGAGCAAGACAGATCTCAGCCCAGCAGATTAACAAGCTTGAAGAACTGTGGAAGGATAACCCTGAAGCTAAGTTAGAAGATCTGGATAAGCCTGGAGTAGATGATGAACCACAACAAGTTCTTCTCAGGTACGAGGATGCTTACCAGTATCAGAACATATTTGGCCCACTTGTAAAACTGGAAGCAGATTATGACAAGAAGCTCAAGGAATCTCAGACTCAAGATAACATTGTTGTTCGTTGGGACATTGGTCTAAACAAGAAAAGGATTGCATATTTCTCCTTTCCAAAAACAAATGATGACATGCGACTGATGCCTGGTGATGAGCTGCGACTGAGATATGTTGGTGAATTGCACAAACCCTGGCAGGGTGTTGGTCATGTCACCAAAGTGCCAAACAACTTTGGAGAGGAAGTTGGAATTGAGTTGCGCAGCAATCTAGGAGCTCCAGTAGAGTGCACTCATAATTTTGTGGTGGACTTTGTGTGGAAATCAACTTCTTTTGATAGAATGCAGACAGGAATGAAGACCTTTGCAGTTGACGAGACATCTGTCAGTGGTTATATCTATCACAAGCTGCTGGGACATGAGGTGGAGGAACAGGTTGTCAAATGCCAGTTGCCTAAAAGGTTTTCAGCCCAAGGTCTGCCAGAGCTTAACCATTCTCAAGTGTATGCCGTGAAGACTGTACTGCAAAGACCACTTAGTCTTATTCAGGGACCCCCAGGCACTGGTAAGACTGTGACATCAGCTAGTGTTGTGTATCACCTGGCCAAGCAAAACAATGGTCAAGTTCTTGTCTGTGCTCCAAGTAACATTGCAGTGGATCAACTGACAGAGAAGATACACAAGACAGGACTCAAGGTTGTAAGACTGTGTGCCAAGAGCAGAGAGGCAATTGACTCTCCTGTAGCCTTCCTTGCACTGCACAATCAAGTGCGTAACATGGACAGTGTTCCAGAATTGCAAAAGCTGCAGCAACTCAAAGACGAGCAGGGTGAGCTGTCTGCTGCTGACGAGAAGAGATACAGGTCCCTGAAGAGGAACTGTGAACGAGACCTGCTGCAGCATGCAGATGTGATCTGTACCACTTGTGTGGGTGCTGGTGACCCTCGCCTGTCTAAGTTCAGGTTCCGTACTGTACTGATCGATGAGTCAACCCAAGCAACTGAACCAGAGTGCATGGTGCCAGTCATACTTGGCTGCAAACAGCTAATCCTTGTTGGAGATCACTGTCAGCTGGGTCCTGTTGTGATGTGCAAGAAAGCAGCCAATGCTGGTCTGTCTCAGTCCCTGTTTGAACGTCTGGTTGTTCTTGGAATCCGCCCCATTCGTCTGCAAGTCCAGTATCGTATGCACCCCGCCCTGAGCGAGTTCCCGTCCAATCTGTTTTATGATGGAACTCTTCAGAATGGAGTCACTGTTGCTGAACGTCAGCAGTCTGGTATTGACTTTCCATGGCCTGTTCCTGACAAGCCAATGTTCTTCTACTCCACCATGGGCCAAGAGGAAATTGCCTCCTCTGGGACATCCTACCTTAACAGAACTGAAGCTGCCAATGTAGAGAAGATTGCCACCCGATTTCTTCGTGCTGGAGTGAAGCCAGAGCAGATTGGAGTGATCACTCCATATGAGGGTCAGAGAGCTTACCTTGTACAGTACATGCAGTTCAGTGGATCTCTTCATGCCAACTTGTACCTGGAAATTGAAGTGGCCAGCGTTGATGCATTCCAAGGACGAGAGAAAGACTACATTATCCTGTCTTGTGTCCGCTCCAATGAACATCAGGGCATTGGTTTCTTGAACGATCCAAGACGTCTGAACGTGGCCTTGACTCGAGCAAAGTATGGCATCATTGTCATTGGCAATCCCAAGATTTTATCCAGGCAACCCCTGTGGAACCATCTGTTGAACTACTACAAAGAGAACAAAGCTTTGATGGAAGGACCCCTGAACAATTTGAAAGAAAGCATGATCCAGTTCAGCAAGCCAAGGAAACTTGTCAACCGCACCAATCCGGGCGGCCGTTTCATGAGTAGCACCATGTTTGATGCCCGTGAAGCTCTAATCCGCGGCAGTGTGTATGACAGGACGATGCCTACAGCACCCATGGACCCAGCTGCCTTCCATGACACTTACTTCCACACTCATGACCGTCTAAGCTACATCGGAGCTGAGCGTACCATCCCACCTGCTGCTGCCGCCAGGATACCGGTACCCGTGGGAATGTTCATCCCCCCTGTACCTCCCCCACACCACTCTTACTTTGGCCAGCCTCTTGCCGGCCGTATGCCTCACGGTCGGCCAGTCCAGCAGCCCCGGCAACGCAATCAGCGAAACCATCACCCTCAGCAGCCAATGGCTTACGCACCTCACATGCCAGCCAGCCAGGCCAGTCAGGATGCTTCCCAGCCACTGTCCCAGGGCCCACTCACTCAAGGTGGTATGTCTATGAGTCAGCCCATGGCTTCACAGCCCTTATCACAGCCGGACCTGTCTCAGGACAGTTACTTGGGAGACGATTTCAACCTCAAGTCTCAAGCAGATGCGGTGTTGTCCCAGGACTCCACCTACCAAGGGGAGAGGGGAGGTTACATGAACTCCTTACCAGACTACTCCCAGCCAAACTATGCCTCCCAGTACTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9EPU0	Regulator of nonsense transcripts 1 OS=Mus musculus OX=10090 GN=Upf1 PE=1 SV=2
Q92900	Regulator of nonsense transcripts 1 OS=Homo sapiens OX=9606 GN=UPF1 PE=1 SV=2
F1RCY6	Regulator of nonsense transcripts 1 OS=Danio rerio OX=7955 GN=upf1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004555 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13086 all species →	AAA_11	AAA domain	Domain	Interproscan
PF13087 all species →	AAA_12	AAA domain	Domain	Interproscan
PF04851 all species →	ResIII	Type III restriction enzyme, res subunit	Family	Interproscan
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

InterPro

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