Gene detail

Detailed information of amic_s0396.g20.t1 in Acropora microphthalma

Genomic Location: sc0000396_pilon:161267...167730
NR annotation: XP_029198235.2, RNA-dependent RNA polymerase 1-like isoform X1 [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

amic_s0396.g20.t1

GCAAAGATGGACCTTTACATGGTGCCAGATGAATTCATAAAGACCCCACCTAAAGACCACTTGATGCAAGCGCTGTATGTAAAACATGTGGAAATTCGCGGAAGATGGGTCCAAGGACCAATGAGATATGACAAAGTCGAGGGAGGGAACCTTATACTAGACTACCTCATATCAGCGAAAGGACCACAGGTAGTTGATACGTTGATGACAGTGACCTTCAAAGACTTGAGACAGCGAAGAGAATATGATTTCGAAGACAAGGCGGAAGAAATCTTGAAAAGGGGAATCTTATTTAGCGGCACAGTGTACCGATTCCTTGGCCATTCCAACTCGCAGCTCAAAGATAGGACCTGTTATCTGATGAATATTACGGATGAAGAAATCTACGATTTGCTCGCACAGTTCGGGGATTTCTCCAAAATCGGGACAGCAGCAAAACGCGCCAAAAGGATTGGACTTTTGTTCTCCTCGTTCACACGAAGCATAAATTTGGAAGAACACGAGTACCGTGTTATTGATGACGTGGAACGCAACAACTACATCTTCACCGATGGCTGTGGATTAATGTCTGAACAGTTTGCGAAGGAAATTCAAGATGTCCAAAAACTCGAAGCCACGCCTAGTGTGGTACAAATTCGCTATCAGGGTTTTAAAGGCGTTCTCCTGCTTCATCGGCAACTAGAGCACCGTCAACAAGTCAAAGTACAATTTCGAAAATCCATGAGGAAGTTTCTTATCCCAGATGAACGCATGCGCAGGACGTGTACCACCTTTGGCGTTGTGCAATGTTCACAGCCTTACACAATTGGTTACCTGAACAAGCAGATCATCATGCTGTTGGTTGACTGTGGGGTGGACCACGGTTTTCTAACAAAGCTACAGAGCGATTTTCACTCCATGTTGAAAGGGCTCGGTCATTCGCGTCAACTCACAGAACAGTATCTGGGTATCAAGGGTGAGATAAAGTTACTGGAAAGGCTGGATAACTACGGCTTGGAGAGCCATAGACTTCAGAAAGACCTGAGAGGTCTCCGTGCCAAAGAAGTCAAGAAAATGCAAAAAGACAACGTGGCTGATGAAACTGACAACGTTGATGCCGCCAGCGCCAGTTCAAAGTGCAAGCTGAGGGTACTGGTACCCAGGTCAAGAATAGTGTTTGCAGTTTGTGATCCACTGAATGAGCTCGAGTATGGCCAATGTATTTTCCAACCAACTATGTTTGACGAGATCCAATTCGCAGAATTTGAAGCGGCAAACGAAGTGATGGTAGTGCGCAATCCATGTTACCATGTGGGTGACATCCGAGTCCTTAAACTGGTGAAAAACAAAGCACAGTACGCGCATCTCAGCGATTGCATCATATTTCCGACGAATGGACGTCGACCACACGCCGATGAATCTTCGGGAGGCGATCTCGATGGCGATGTGTTCTTCGTAAGTTGGGACTCTGACCTGATTCCTCAATGGCGGAGTTCCCCGTTCGACTATTCAACCAGCAGCCCTCTTGTCGCTATTCCTAACGCGATTAAAAAGTACTGGGAGCAGCTCACCAAGCCACTGACCAAGCGCATTGCCGACTGGGGTCATGAGTCGATGCCGTTCTTGTTTGGCACACAGCAGCAAGCCGAGAAAGAAAGGAAACAGACGGAAAGGCGACACATGCTCGAGTATTTCACTAGTTACAACAACTATTTGGTGGGGCGCGTGGACTCCATTTTCATGAAGTACGCTGCACTTTACGGTCCTTCCTGCAGTGAGTGTGTTTATCTAAACAGGTTCTTTTCGGATGCAGTGGATATGGTAGCATCTAAGATGTTAATAGAGGCTGAACTTCGAAATCTGGAGCGCGAGTATCATAGAAAAGTGGCACAGTTGCCATCTCACCATCATCCTCAATCTTCGGGATGGCTGTCGTTCCTAATCGGAAAACAAAAGCCACCTTTCCGACCTGGCGATGATTTGTGGACGCGAATGGAAGAAAGAACTAAAATATTCGTGGATGAAATGTCGATGAGATCGTAG

Transcript

amic_s0396.g20.t1

AGCAAAGATGGACCTTTACATGGTGCCAGATGAATTCATAAAGACCCCACCTAAAGACCACTTGATGCAAGCGCTGTATGTAAAACATGTGGAAATTCGCGGAAGATGGGTCCAAGGACCAATGAGATATGACAAAGTCGAGGGAGGGAACCTTATACTAGACTACCTCATATCAGCGAAAGGACCACAGGTAGTTGATACGTTGATGACAGTGACCTTCAAAGACTTGAGACAGCGAAGAGAATATGATTTCGAAGACAAGGCGGAAGAAATCTTGAAAAGGGGAATCTTATTTAGCGGCACAGTGTACCGATTCCTTGGCCATTCCAACTCGCAGCTCAAAGATAGGACCTGTTATCTGATGAATATTACGGATGAAGAAATCTACGATTTGCTCGCACAGTTCGGGGATTTCTCCAAAATCGGGACAGCAGCAAAACGCGCCAAAAGGATTGGACTTTTGTTCTCCTCGTTCACACGAAGCATAAATTTGGAAGAACACGAGTACCGTGTTATTGATGACGTGGAACGCAACAACTACATCTTCACCGATGGCTGTGGATTAATGTCTGAACAGTTTGCGAAGGAAATTCAAGATGTCCAAAAACTCGAAGCCACGCCTAGTGTGGTACAAATTCGCTATCAGGGTTTTAAAGGCGTTCTCCTGCTTCATCGGCAACTAGAGCACCGTCAACAAGTCAAAGTACAATTTCGAAAATCCATGAGGAAGTTTCTTATCCCAGATGAACGCATGCGCAGGACGTGTACCACCTTTGGCGTTGTGCAATGTTCACAGCCTTACACAATTGGTTACCTGAACAAGCAGATCATCATGCTGTTGGTTGACTGTGGGGTGGACCACGGTTTTCTAACAAAGCTACAGAGCGATTTTCACTCCATGTTGAAAGGGCTCGGTCATTCGCGTCAACTCACAGAACAGTATCTGGGTATCAAGGGTGAGATAAAGTTACTGGAAAGGCTGGATAACTACGGCTTGGAGAGCCATAGACTTCAGAAAGACCTGAGAGGTCTCCGTGCCAAAGAAGTCAAGAAAATGCAAAAAGACAACGTGGCTGATGAAACTGACAACGTTGATGCCGCCAGCGCCAGTTCAAAGTGCAAGCTGAGGGTACTGGTACCCAGGTCAAGAATAGTGTTTGCAGTTTGTGATCCACTGAATGAGCTCGAGTATGGCCAATGTATTTTCCAACCAACTATGTTTGACGAGATCCAATTCGCAGAATTTGAAGCGGCAAACGAAGTGATGGTAGTGCGCAATCCATGTTACCATGTGGGTGACATCCGAGTCCTTAAACTGGTGAAAAACAAAGCACAGTACGCGCATCTCAGCGATTGCATCATATTTCCGACGAATGGACGTCGACCACACGCCGATGAATCTTCGGGAGGCGATCTCGATGGCGATGTGTTCTTCGTAAGTTGGGACTCTGACCTGATTCCTCAATGGCGGAGTTCCCCGTTCGACTATTCAACCAGCAGCCCTCTTGTCGCTATTCCTAACGCGATTAAAAAGTACTGGGAGCAGCTCACCAAGCCACTGACCAAGCGCATTGCCGACTGGGGTCATGAGTCGATGCCGTTCTTGTTTGGCACACAGCAGCAAGCCGAGAAAGAAAGGAAACAGACGGAAAGGCGACACATGCTCGAGTATTTCACTAGTTACAACAACTATTTGGTGGGGCGCGTGGACTCCATTTTCATGAAGTACGCTGCACTTTACGGTCCTTCCTGCAGTGAGTGTGTTTATCTAAACAGGTTCTTTTCGGATGCAGTGGATATGGTAGCATCTAAGATGTTAATAGAGGCTGAACTTCGAAATCTGGAGCGCGAGTATCATAGAAAAGTGGCACAGTTGCCATCTCACCATCATCCTCAATCTTCGGGATGGCTGTCGTTCCTAATCGGAAAACAAAAGCCACCTTTCCGACCTGGCGATGATTTGTGGACGCGAATGGAAGAAAGAACTAAAATATTCGTGGATGAAATGTCGATGAGATCGTAGCATGTTCGTATGATTACGCCCGTGTAACTGTCCACCGACACTCGGGGCAAACTTCGTACTGAGTGAAAAACCCGCTCAAGAAAAATTAATTAAAAAATGGAACGAACACAAAAATGACAAGGAAGGAGCGTAGATCGATGGTTATCTTCAAGGTACTAAGAAAAAAAACTAGCTCCAGAAATACAGTAACTAtcggctatgccatgctggtaagaagcccgaaaaagcagtccatggttgcctgatacctgccaggtgatacggttgtgcgcatgcataaggtgatggccgcaacacgcagctggtgtaagcatgtgtctgtccaccttgcattttttttctacAGCCGAGAAATAAAATTCCATTTTGTCA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9LQV2	RNA-dependent RNA polymerase 1 OS=Arabidopsis thaliana OX=3702 GN=RDR1 PE=2 SV=1
Q0DXS3	Probable RNA-dependent RNA polymerase 1 OS=Oryza sativa subsp. japonica OX=39947 GN=RDR1 PE=2 SV=2
O82504	RNA-dependent RNA polymerase 2 OS=Arabidopsis thaliana OX=3702 GN=RDR2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001364 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05183 all species →	RdRP	RNA dependent RNA polymerase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007855 all species →	Family	RNA-dependent RNA polymerase, eukaryotic-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23079 all species →	RNA-DEPENDENT RNA POLYMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003968 all species →	Molecular Function	RNA-dependent RNA polymerase activity	Interproscan
GO:0030422 all species →	Biological Process	siRNA processing	Interproscan
GO:0031380 all species →	Cellular Component	nuclear RNA-directed RNA polymerase complex	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

No KEGG orthology assignment for amic_s0396.g20.t1.

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 Acropora microphthalma 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 Acropora microphthalma, 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 →