Gene detail

Detailed information of alvinactis_v1_g14070 in Alvinactis idsseensis sp. Nov.

Genomic Location: chr_7:2833051...2848082
NR annotation: XP_020901800.1, poly(A) polymerase type 3 [Exaiptasia diaphana]
Species Alvinactis idsseensis sp. Nov. · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

alvinactis_v1_g14070

ATGTCCAGCTCAACAAATACCACCAACCCGACACAGAAAACCTTTGGCGTTACATCAGCCATAAGCCATGCGAAACCCAAGCCAAGAGACTTTGAGCTCACCAAGAAGCTCGGAGAATCTCTTGTGCCCTTTGGCGTCTTCGAATCGGACGAGGAGCTACAGCACCGTATGACTGTTCTTGGTAAACTGAATGAGATTGTGAAACAATGGATAGTAGACATCAGTCTTCAGAAGAATATGCCTGAAAATGTAGCCCACTCAGTTGGAGGAAAGATATTCACATTTGGTTCTTTCCGTCTTGGGGTGCATACTAAAGGTGCTGATATTGACACTCTTCTTGTTGCACCTCGACATATTGAACGGTCAGACTTTTTCTCCACGTTTTATGATCTCCTCAAAAATCATGAAGACGTGAAGGAACTGAGGGCTGTGGAGAATGCTTTTGTTCCTGTCATCAAACTTATATTTTGTAACATCGAGGTTGATCTACTGTTTGCTCGTTTGGCATTACCAGAAGTACCAGACAATCTGGACTTACTTGATGAGAACATGCTGAAGAACCTTGATCCCAAGTGTGTCAGGAGTTTAAATGGTTGTAGAGTCACAGACGAGATCTTGAGACAAGTGCCCAACATTGAAAACTTTAGGCTTACTTTGCGAGCTGTTAAGTTATGGGCAAAAAAACGTAGCATCTACTCCAATGTGTTAGGGTTTCTCGGCGGTGTTTCCTGGGCAATGCTTGTGGCAAGAACATGTCAACTCTACCCAAATGCTGTAGCTTCTACTTTAATTTTAAAATTCTTTCTTGTGTTTTCGAAATGGCAATGGCCCAACCCTGTTCTACTAAACCAAATTCCAGTTCCCTCTGAAAATAAACTAGGATTTCAAGTGTGGGATCCTAGaACCAATCCATCAGATCGTTATCATCTTATGCCTATCATCACACCAGCCTATCCACAACAGAACTCTacatttaatgtatccatgtcgaccagacaagtcatggaagaagagttttatatagGACTTAAAAACTCTGAGGACGTTCAAAATGGCAAAGCAAACTGGGAAATCTTGTTTGCACCCACTAATTTCTTTTTAAAATACAAACATTATATTGTGCTAAGTGCTTGTGCCGCAAGTGAAGAAAACCATCTAGAATGGATTGGTTTAGTCGAGTCCAAAGTTAGAACACTGGTCCTGAGTTTAGAAAACAATACTTACATAAAACGAGCTCATGTGAACTCTACCAGTTATGGACCACTGGACTCAGAAAAAGATACATTTTTGACAAGGTGGTTTATTGGACTATTATTCAATAAGGCTGAAAATGTCAATATTAATCTCACCAATGAAATACAGATGTTCACAAATACAGTTCATAATCAAGCAGTTAGCACAAAGATGTTGAAGGATGGTATGAAAATAGAAGCTCAACATGTAAAGAGAAAACAAGTCAACAAGTTCTTACCTCCTGGAGTATTTAAGCCGAAGAAGAAGAGCGGAGTGtgtgtcgatgataaagccaacacttcCAAGGGTGATCAAAGCTTTAATGAAAGCTCAGACAGCTTCTCTGAAGTGAGAGAAGAACAACCAGAGATAAAGGACAAGGATGAAAAAAATTCATCAGAGGAACAAAAACCAGAGACATCCACAAACAATGAGACCGCACCCAAGACACCCAACACGACATCACAACAGCCACCAAGTATCGAAACTAAAGGCGAAGTGACGTCATCAACACCTACAGCTACAAGTACACCCCCTTCAAGCCAAGCACTCCCCAATAATAACACATCACCAACCACTAGTACTAATAGTACACAAGACAGCTCACGGCATGCAATCAAGAGACCTAGTTCTCCACTAGATCAGGTAGCTAAAGCAAAGCGAATGAGAACAGAAAGTACTACGCAGTCAGACGTTCAAACTGGTTCAAAGGAAAATAATGCAGATAGTAGTCATCCTGAAGTAGAACAAAATGATGACAAAATGAGCGACGGGCAAGAGGTGACTAAAAACTCAGAGTCTGAACCAAGTGCAGAAACCAGAGGAGTAAAGAGACGAAGCTCCGGCCCTATAGAACAGAGTATCATAAAACATATCAAAGAAAGTAGTCAGGAGGATGAAGAAAAAGAACTGTATGACACAACGGAACAGCTACAAGCTTCTCAGATACAAGTCCCTCTTAAGAACTCTATAAAACTTAAACTCAAATAA

Transcript

alvinactis_v1_g14070

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P25500	Poly(A) polymerase alpha OS=Bos taurus OX=9913 GN=PAPOLA PE=1 SV=3
P51003	Poly(A) polymerase alpha OS=Homo sapiens OX=9606 GN=PAPOLA PE=1 SV=4
Q61183	Poly(A) polymerase alpha OS=Mus musculus OX=10090 GN=Papola PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001946 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04926 all species →	PAP_RNA-bind	Poly(A) polymerase predicted RNA binding domain	Domain	Interproscan
PF04928 all species →	PAP_central	Poly(A) polymerase central domain	Domain	Interproscan
PF20750 all species →	PAP_NTPase	Poly(A) polymerase nucleotidyltransferase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007010 all species →	Domain	Poly(A) polymerase, RNA-binding domain	Interproscan
IPR014492 all species →	Family	Poly(A) polymerase	Interproscan
IPR043519 all species →	Homologous_superfamily	Nucleotidyltransferase superfamily	Interproscan
IPR007012 all species →	Domain	Poly(A) polymerase, central domain	Interproscan
IPR011068 all species →	Homologous_superfamily	Nucleotidyltransferase, class I-like, C-terminal	Interproscan
IPR048840 all species →	Domain	Poly(A) polymerase, nucleotidyltransferase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10682 all species →	POLY A POLYMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004652 all species →	Molecular Function	obsolete polynucleotide adenylyltransferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006378 all species →	Biological Process	obsolete mRNA polyadenylation	Interproscan
GO:1990817 all species →	Molecular Function	poly(A) RNA polymerase activity	Interproscan
GO:0016779 all species →	Molecular Function	nucleotidyltransferase activity	Interproscan
GO:0031123 all species →	Biological Process	RNA 3'-end processing	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
K14376	PAP; poly(A) polymerase	EC:2.7.7.19	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 Alvinactis idsseensis sp. Nov. 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 Alvinactis idsseensis sp. Nov., 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 →