Gene detail

Detailed information of ANN32768-RA in Montipora grisea

Genomic Location: Scaffold_1836__1_contigs__length_49034:37754...43637
NR annotation: RKU17849.1, DNA-directed RNA polymerase subunit beta' [Candidatus Poribacteria bacterium]
Species Montipora grisea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ANN32768-RA

ATGAATACAGCGTTTGACAGTATCTCGATAAAAATAGCCTCACCTCAGGAGATTAAAGCGTTATCAAAGCAGACCTGTTGCAAGCGCCGGAGCACATCTCAAACGACAGGAGCGCCCTTTATCTGTCCGGAGATGGGAAGGTGTAACTGCGGCGAGGTCAAGAAGGCGGAGACAATTAATTATCGCTCCTTCCGGCCTGAACCGGATGGGCTCTTCTGCGAAGCTATCTTCGGCCCGCAAAAGGACTTTGAGTGTAGTTGTGGGAAATATAAACGGATTAAGCACAAGGGAGTGATATGTGATCGGTGTGGCGTTGAGGTAACACAGCAGCGCGTCCGCAGACAGCGCCTCGGTTATATCCAACTCGCTGCCCCTGTTTCTCATATATGGTTCTTCAAAGGCATTCCGTCGCGGATTGGCACCTTTTGTGAACTCTCTTCACGCCAAGTAGAACGCGTCATCTATTTTGAAGCGTTTATCGTTGTAGAAGTAACCGACCCCGACTGTCCGCTTCAACCGCGCCAGGTATTAACAGAGTTAGAGTACGAGAACGCGAAACAACAGTACCCGGGGCAGTTTCGCGCGGGTACTGGCGCAGAAGTGATTGCTGAGATTCTGAAGAGCATAGATATGCAGGCAGAGATAGAGAAACTCACTACTGACCTGGAGGAAACAACAAGTCATCAGAAAAGGCTCAAGATAACGAAACAGCTCAAACAGTTGTCTGACTTTGTTGCATCTGAACAGCGACCGGAGTGGATGATTATGGATGTGATTCCAGTCATTCCGCCGGACTTACGGCCCCTGGTTTCCCTAGAAGGTGGGCGTTTTGCCACGAGCGACTTGAATGATCTGTATCGCCGCGTGATTAATCGTAACAACCGACTGCGTAAGTTAATGCAGCTCCGCTCCCCGGAAGTCATTTTGCGCAACGAAAAACGGATGTTGCAGGAAGCTGTTGATGCCTTCTTTGACAACGGGCGGCACGGCAGGCGTGTGACAGGCCCTGGCAATCGGCCCCTCAAGTCACTTTCCGATATCCTCAAAGGTAAGGTTGGGCGGTTCCGCCAGAATCTGCTCGGAAAACGTGTTGATTACTCCGGGCGTAGCGTCATCGTGGTCGGCCCCGAATTGGGACTGCACCAATGCGGCTTAACCCAAGCGAATGGCGGTCGAACTAGACTGCAAGCATACGGCCATACGCAGACAATTAAACGGGCGAAACACATCGCCGAGCATGTTGATTCCGATTCACCCGTCTGGGATGTCTTGGAGGAGGTGATTGCCGAGCATCCTGTGTTGCTGAATCGCCCACCGACGCTGCACAGACTCGGCATTCAGGCGTTTCTGCCTGTGTTAGTGGAAGGCAAATCGATTCGGATTCCCCCCCTTGTGTGTAAGGCATTCAACGCCGATTTTGACGGAGACCAGATGGCGGTGCATGTACCCCTCACTGTCGAGTCACAGGCGGAGGCAAAACTGCTGATGCTCAGCAGTCATAACATCCTCAAACCTTCACATGGAGGGCCGATTGCTGTGCCAGAGCTTGACATGGTACTCGGTCCCAGTTTCTTGACGAAGGAACTACCGCAACATGCGGAAGATGCGGCACTCCTGCATGAGGTTTGGTCTGGAAATAGTCCTAACCCCTCTTCAGAGCTCCTAGAGCAGCTCCGCCAAAAACCGTGGTACCACCGTCGCTATCTGCATCCAGAAGAGGTTATCGCGGTACATACAGCCGGTCAACTCAAACTGCACGATAGCCTTCAACTCTTTTTTAATCGGCACAATGGAGAGAGCGTAGAGCCGATTCTCACCACGGTCGGCAGGGTGATTTTCAACGAAGTGCTTCCAGATAAACTGAAGCAAAAGAAAGCGAACTCATCCGAAGATCCATGGGTAGACGCGCATTCAGGGCAACAGGTGCCTTTTTTCAACGCCGAAGCCGGCGGCCACGAGTTATCCAAGATTGTCTACGACTGTTTCAATGAATTGGGAACGCGGGACACAGCAAACGTTCTTGAAGAAATTCAAAAACTTGCTTTTCACTATGCAACCCTGAGTGGCATATCCCCCTGCATAATGGATTACCTCACACCGGACAACCGGGACGCTTTAGTGAGCAAAGCGCAGTCAGAAGTGGATAACCTCCTTGCTACAACCTCCGCTACAGACACAGGGGAGTTAGAGAACGAGCGAATTCGTATCTGGCTCGAAGCGATTGGAGAGGTTGAGGACACCATGTTCTCTACCTTACCCGAATTAGAAACATCGCTCGTTGAACGTGGCGACTCGAGGAAGATCCATCCCTATGTTGATCCGAACGGTGTAGAGACACGCGCCCAAACAGTAAAAGGCTTCAGTCCAGTACATATCATGGCGGATAGTGGAGCGAGAGCGCGGAAAAACCCGTTTATGCAAATTAGCGCGATTGTTGGGTTAAAATCCGATCAGAGCAACAACATCCTCTCCACACCCATTACTGCTTCCTATCGCGAAGGCTTAGATGTGTTAGATTATTTCAACTCCACCTACGGTTCGCGCAAAGGCTTGGTGGATACCGCCATGAAAACTGCCGCATCCGGTTACCTAACCCGGAAATTAGTGGATGTTGCACAAGATGTCCGCGTGACTACTGAAGATTGCGGGACGCTCAACAGCATTCAGAAGTTTACGACTGACGGAGGAACTCTCGCATTTAAAATCAGAGGGCGTACTGCCGCCGAAGATATCATCCACCCGGATACAGACGAAGTGCTGGTGAACAGCGAGCAATTGATATCAGAGGAAGAGGCGACACAAATCGAGGCCGCTGGCATCAAAGTGGTAAAAGTGCGCTCAGTACTCACCTGTCAAGCCCAGGACGGTGTCTGCTCAAAGTGCTATGGGATTGATTTAACGACCAACAATCTTGTCAATGTCGGCGAAGCCATCGGCATCATCGCTGCACAATCCATTGGGGAACCCGGCACGCAGCTAACGATGCGGACGTTCCACACCGGTGGGGCTGTTGAGGAGATTTCGGATGCACGCCAGCGCAGAGTGCTTGCGAAAATCAACGGGAGCGCGCGATTCCGCGATTTCCGACCCGGCAGCACAGTGCGTCAAGAAGGTGAACTCTGGATAGTCATCGGTTCTGACAGTCCATCTTCTACGTGGGCGGAAGAGCAGGCTGACTTGAGGAACGCCATCAGCAGGCCTGCCAACCGCGCAAACCTGGATGCCCCTGCTTACAAGGTCACCCAGGTCAACCACCCCGAGTGCCAATTGCGTCCAGGCGAGCTCTTGAGTGAGAAACAGTGGACTGAAAACGAACGACGCTTTAAAGGCTTTAGCACCGATACATGGCAGTATCAGGTAACTGCTGTATCGGATAGTGCCTGCCACCTTGAGATAGACGACCGGCTGTCACAGGCAGAATATGAAAAGGCACGGGAACAATACGGATTTCACCACTTTGTAACGCCGAAATACCGCGTAGCGCAAGTGCACCATCGCGATATCTCCTTGACTCGCGGCGAGCTGCTCACAGCAAAAGCCGCTGAGGAGGAGAAGGCGAAGATCCGGGCACAATTTGATGGGGAATGGTTTTACCAAGATTCAGAAACAGGAGAGCTCTTTACCAAAGCAGAACTGGTTGCAAAGGTCGAATCAGACAACCGACCTGCTAACTGGGTGGACGACCCATCGAACTTAAATCCCCCAGTCAGATCTTCTGTAGAAGCGAATCTTGAATCACAACAACCGCCAGGGGAAACAGAAAACCTGCGAAGCGAGACAACTGCATTTGAGCGAGTAGGAGATCCAGTGCAAGAGGAAACTATCGCCCCGTGGCTTACCCCATTTGACTTAGAGTCAAAGCCTGTCTACGTTGTGCATGCTGAGATAACAGCAGGCGAGAACTCAGGGTTGGATCCAGCCGATTATCAGATTGGAAGAGAATTAACCGAACGCGCCTACGAGCATGCACGTGTAAGGTATCAGGCGTTTAAGGTTGAAAAATCGGATGCTCCGCAGCACTATGTCACCGAAGTCCATCACCCTGAGTGTCCATTTGAGATCGGCGAAGTGTTAGCAACGGACGCAGTAGAGAAGGCACACAAACGATTCGCTGGGTTCAATGTTCAAAAATTGAAACACCGCGTCATCCATGTGCATCATCCAGACTGCACGCTCAAACCGGGCGACTTGCTCAGCGATAGTGAAAAGAAAGAGTACAAAACTACCTACCCCAGCATTGCAGCGTCCTCCGCTGTCAACACATCAGGGGGCTTTGAGACAGAACGGCTTTATCGTGTTACTGCTGTCAATCACCATGACTGTCCGCTACAGCCTGGCGAACTGTTGACGCAACAGGTTTCAAACGCACATCGGCGGCAGTACAAGGGGTTTGAAGTAGCGCGCCACTACGAGGTAACGCATGTCGAAGACGGTACTACATCTGTGACTGCCGGTCAACGTTTAACAGAGAGCGAGTATAAGGCGTTGCGCAAAACAGATGCCGCGCTCGTGGAGAAAGTCACAAGCTGGTACCAGGTCGTTAGTGTACATCACCCTGACCTCGATTTAGAAGTGGGAACGGAATTGACTGAAAAGGAATACCGGGCCTACCAGCGGCAGTACAAAGCGTTTGAGGTTGAAAGAGTCTATCGGGTAATTGAGGACAAAAGGACGGATGCTGGAGAAGGGGTTTCCAACCCCGAAGTCCAAACGTTCGCATCTGGGCATATTCTCAGTGAAAAGGAACACCGCGCACTACAGAAGGAAAACCAGCGGAAAACCTATACCGTCACTGATATCTACCACCCCAATTGTGGGCATACTGTGGGCGAGGAGTTGTCTGAAGAAGCATACCAGAACACCACTGAGCACTACGCAGGCTTTGACACAGCCGAGCTCGACTTGCGCATGCATATCGAGATAGTGGAACCTGACGGTTCTTACGTGCCACATCTCATTCCTGCAGGTTACTCCTTCTCCATCGAAGAAGGGGATGGCGTTAATAAAGAAGATGCACTCGCAGAACTTCACGAAAAAACGGCCAACCGCGACATTGTTGCAGGCATACCGCGCGTCACGGAACTGTTTGAAGCGCGGAGGCCCAAGCGCGAGGATGCCGCAGAAATCGCTGAAATTGAGGGATACGTACGAGCTGCTGGCACCAAGGCTGGTGTTCCCACATACCACATCGAAGACGAAGGGCATACCAGCAAGGTCTATGCTATCCCTGATGAAAAACGGCGCGTCACTGAAGGCGACTGGGTGGATGCTGGCCAACCCCTCACCGACGGATTCCTCAACCCGCACGATATTTTAAAAATCGGGCGCACCATCATGGATGGGGTACCGGTTGAAGGAGAAGAAGCTGTCTGGGCATACCTTGTTGATGAAGTCCAGAAGGTCTACGGCGCAAGAGTCATCAACGATAAACATATTGAGACCATAGTTCGGCAGATGTTAACCAAAGTCCGCATCACCGAATCAGGCGATACAGGTTTCTACCCGAACGAGGAGGTACAACGCGACAGTGAAGTTGAATCCACGGGCGGCACGCCGGCCACAGGTGAACCCATTCTCCAGAGTATCAGCAAAGCCTCCTTGAGCACCGATAGCTTCATTTCGGCTGCCACCTTCCAGCAGACGACGAAGGTCCTCACAGACGCGGCAGTCAGTGGGCAAACCGATAGGCTCTTCGGCCTCAAAGAAAACGTCATCCTCGGCAGGCTCATCCCTGCAGGGAGCGGCTTCCTCCGAATTTCAAAACCTAGAGGTATCCTACCAAAGCCAGCAGCTTGA

Transcript

ANN32768-RA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q39Y12	DNA-directed RNA polymerase subunit beta' OS=Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15) OX=269799 GN=rpoC PE=3 SV=1
Q3A9Q8	DNA-directed RNA polymerase subunit beta' OS=Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) OX=246194 GN=rpoC PE=3 SV=1
B9M6V1	DNA-directed RNA polymerase subunit beta' OS=Geotalea daltonii (strain DSM 22248 / JCM 15807 / FRC-32) OX=316067 GN=rpoC PE=3 SV=1

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04983 all species →	RNA_pol_Rpb1_3	RNA polymerase Rpb1, domain 3	Domain	Interproscan
PF00623 all species →	RNA_pol_Rpb1_2	RNA polymerase Rpb1, domain 2	Domain	Interproscan
PF04998 all species →	RNA_pol_Rpb1_5	RNA polymerase Rpb1, domain 5	Domain	Interproscan
PF04997 all species →	RNA_pol_Rpb1_1	RNA polymerase Rpb1, domain 1	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006592 all species →	Domain	RNA polymerase, N-terminal	Interproscan
IPR042102 all species →	Homologous_superfamily	RNA polymerase Rpb1, domain 3 superfamily	Interproscan
IPR007066 all species →	Domain	RNA polymerase Rpb1, domain 3	Interproscan
IPR000722 all species →	Domain	RNA polymerase, alpha subunit	Interproscan
IPR012754 all species →	Family	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Interproscan
IPR038120 all species →	Homologous_superfamily	RNA polymerase Rpb1, funnel domain superfamily	Interproscan
IPR007081 all species →	Domain	RNA polymerase Rpb1, domain 5	Interproscan
IPR044893 all species →	Homologous_superfamily	RNA polymerase Rpb1, clamp domain superfamily	Interproscan
IPR007080 all species →	Domain	RNA polymerase Rpb1, domain 1	Interproscan
IPR045867 all species →	Family	DNA-directed RNA polymerase, subunit beta-prime	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19376 all species →	DNA-DIRECTED RNA POLYMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003899 all species →	Molecular Function	DNA-directed 5'-3' RNA polymerase activity	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	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
K03046	rpoC; DNA-directed RNA polymerase subunit beta'	EC:2.7.7.6	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 Montipora grisea 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 Montipora grisea, 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 →