Gene detail

Detailed information of evm.model.contig_28207.1 in Platygyra sinensis

Genomic Location: contig_28207:1014...21712
NR annotation: no NCBI-NR hit recorded
Species Platygyra sinensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.contig_28207.1

ATGCTCAGAACAGCCCATGCAGCAGGAGCTTCTACACAATCGGCTATTCTCAAATTTATTGGAGAGAGATTTAGAATAAAGATGAGATTACCAGACTGGTACACAGATGAAGAGGTGGCTCATTATGTTCTACAAAAATGTGTTTGTGTTCACCTGGATGGAAATATGGACAAGTTTAATTTATTGGTTTTTATGGCAAGAAAGCTGTATGCATTGGCACTAGAAAAATGCGCCCCAGAGTCAGCTGATAATCCTATGATGCAAGAAGTACTTCTTGGTGGTCACTTGTATCTCATGTGCTTAAAGGAAAAGTTAGAGCTTTGGCTATATCGAGTGCGAGAGGCCCTTGAAAAAGCTATGACAAAAAAGAGAGATTTCCATTTAAATACAGCAACTTTACTACAAGCAATGCAATTTGGTGTGAACATATCACACCAAATGGAATATCTTCTTGCTACTGGAAATCTGGTATCAAGATCAGGTCTTGGACTTATGCAGGTCTCAGGATTTTCAGTTGTAGCAGACAGGCTCAACTTTTACAGGTTCCTGTCCCATTTCCGCTGTGTCCACAGAGGTTCTTTCTTTTCTCAGATGAGAACAACATCTGTCAGAAAATTATTGCCTGAAGCCTGGGGTTTTCTGTGTCCTGTTCATACTCCAGATGGTGCTCCTTGTGGATTGTTGAACCACATGGCTGCGTCCTGCAAGGTTGTGAATACTGTACCACAGACTGCCCATCTCTCCAGACTCCTGTGTTCATTAGGGATGACTCTGAATGACGCCCCAGCACCTGTTGATATGAAGTCTTGTTATACAGTTATATTGGATGGTAGAGTCCTCGGCAGACTCGATATGGACCATGCTCCAGCTCTTGTAAACAGGCTCCGCATGTTAAAAGTACTTGGACAAGAAAAGGTGCCTCAGATGTTAGAGATATGTCTTGTGCCCATTACAAGTGTAGCCAGTCAGTATCCTGCCCTTTACCTCTTCTCCACTCCAGCTCGGATGATGAGGCCGGTTCTCAACCTGGCAGCTGGGAAAGTGGAAATGATTGGCACTTTTGAGCAGGTTTATATGAACATTGCTGTTATCCAAGAAGAATCTCACGAAGGGGAAACAACTCACCTTGAATTGAAACAGACAAGCATGTTGAGTGCTGTTGCAAGTTTAACTCCATACTCTGACTTCAACCAAAGTCCTCGTAACATGTACCAATGTCAGATGGGAAAACAAACGATGGGAACACCAGCGCAGGCATTGAAACACCGGGGTGATAACAAACTGTATAGGATACAGACACCGCAGAGTCCTCTGGTAAGACCCGCTGCACATGATGAGTTGGCCATTGATAACTACGCTTTAGGAACAAATGCTGTTGTGGCTGTTATCTCTTACACGGGTTATGATATGGAAGATGCAATGATCCTTAACAAAGCGTCATTTGAGCGCGGGTTCGCTCATGGCACCGTGATAAAGTGCGAGATAGTTGATCTTATCAAAATCTCTGGAAACACGAAAGCTTCAAGCCTCAGATTTGGCTGTCTTCCTGATGATAAACGAGTCGAAGGATTTCTCGACTCTGATGGTCTGCCACCAATTGGAGCCAAGCTGGAGACAGGAAACCCATATTACTGTTACATTGACGACAATACCGGTCAAGCAAACATCAAGAAATACAGCAGCTTGGAAAACGCGATCGTTGACGATGTAAGAATTCTTGGCAATGACGATGGCACTGGTTCACTTCAGAGAGCGGCTATTAAATTGAGAATACAGAGAAACCCAATCATTGGAGACAAGTTCTCAAGTCGGCATGGACAGAAAGGAATTTGTAGCCAGAAATGGCCAATTGAGAATATGCCTTTTACAGAATCTGGCATGACTCCAGATATCATATTTAATCCACACGGCTTCCCTTCTCGTATGACAATCGGTATGATGATAGAGAGTATGGCTGGTAAATCCGCCAGTCTCAATGGACTTGCATATGATGCTACACCATTTACCTTCTCAGAGGAGGATCCTGCTATTGATTACTTTGGAAACCTCTTAAAACAATCCGGGTACAATTACTACGGCACAGAACGAATGTACAGTGGCACGGACGGCCGTGAGTTTAAAGTTGACATATTTTTTGGAGTGGTTTACTATCAGCGACTGAGACACATGGTGGCAGACAAGTATCAGGTTCGGACAACAGGCCCCATAGACATACTAACACATCAGCCAGTACAGGGTCGTAAAAGACAAGGAGGCATTCGGTTTGGTGAGATGGAGAGGGATGCGCTCCTCGCGCATGGTACCTCTTTTCTGTTGCAAGATCGACTCATGAACTGCTCAGACAAAACAGTGGGTCAGGTGTGTACCAAGTGTGGCAGCATACTATCCCCTCTCCTGGACAAACCTGCCGTCGAGTTGGCAGCTGCGGCTGCGCACAGAGAACGGAAGTGGACTTGCAAAACTTGTGAAAGCAGCGAACACATTCAGCTGTTAGCCTTCCCTTACGTCTTCCGTTATCTTGTGGCCGAGTTGGCGGGCATGAATATCAAGACGTCGTTGGAAGTGAAAAGAGTTGGGACTTAA

Transcript

evm.model.contig_28207.1

ATGCTCAGAACAGCCCATGCAGCAGGAGCTTCTACACAATCGGCTATTCTCAAATTTATTGGAGAGAGATTTAGAATAAAGATGAGATTACCAGACTGGTACACAGATGAAGAGGTGGCTCATTATGTTCTACAAAAATGTGTTTGTGTTCACCTGGATGGAAATATGGACAAGTTTAATTTATTGGTttttatggCAAGAAAGCTGTATGCATTGGCACTAGAAAAATGCGCCCCAGAGTCAGCTGATAATCCTATGATGCAAGAAGTACTTCTTGGTGGTCACTTGTATCTCATGTGCTTAAAGgAAAAGTTAGAGCTTTGGCTATATCGAGTGCGAGAGGCCCTTGAAAAAGCTATGACAAAAAAGAGAGATTTCCATTTAAATACAGCAACTTTACTACAAGCAATGCAATTTGGTGTGAACATATCACACCAAATGGAATATCTTCTTGCTACTGGAAATCTGGTATCAAGATCAGGTCTTGGACTTATGCAGGTCTCAGGATTTTCAGTTGTAGCAGACAGGCTCAACTTTTACAGGTTCCTGTCCCATTTCCGCTGTGTCCACAGAggttctttcttttctcagatgAGAACAACATCTGTCAGAAAATTATTGCCTGAAGCCTGGGGTTTTCTGTGTCCTGTTCATACTCCAGATGGTGCTCCTTGTGGATTGTTGAACCACATGGCTGCGTCCTGCAAGGTTGTGAATACTGTACCACAGACTGCCCATCTCTCCAGACTCCTGTGTTCATTAGGGATGACTCTGAATGACGCCCCAGCACCTGTTGATATGAAGTCTTGTTATACAGTTATATTGGATGGTAGAGTCCTCGGCAGACTCGATATGGACCATGCTCCAGCTCTTGTAAACAGGCTCCGCATGTTAAAAGTACTTGGACAAGAAAAGGTGCCTCAGATGTTAGAGATATGTCTTGTGCCCATTACAAGTGTAGCCAGTCAGTATCCTGCCCTTTACCTCTTCTCCACTCCAGCTCGGATGATGAGGCCGGTTCTCAACCTGGCAGCTGGGAAAGTGGAAATGATTGGCACTTTTGAGCAGGTTTATATGAACATTGCTGTTATCCAAGAAGAATCTCACGAAGGGGAAACAACTCACCTTGAATTGAAACAGACAAGCATGTTGAGTGCTGTTGCAAGTTTAACTCCATACTCTGACTTCAACCAAAGTCCTCGTAACATGTACCAATGTCAGATGGGAAAACAAACGATGGGAACACCAGCGCAGGCATTGAAACACCGGGGTGATAACAAACTGTATAGGATACAGACACCGCAGAGTCCTCTGGTAAGACCCGCTGCACATGATGAGTTGGCCATTGATAACTACGCTTTAGGAACAAATGCTGTTGTGGCTGTTATCTCTTACACGGGTTATGATATGGAAGATGCAATGATCCTTAACAAAGCGTCATTTGAGCGCGGGTTCGCTCATGGCACCGTGATAAAGTGCGAGATAGTTGATCTTATCAAAATCTCTGGAAACACGAAAGCTTCAAGCCTCAGATTTGGCTGTCTTCCTGATGATAAACGAGTCGAAGGATTTCTCGACTCTGATGGTCTGCCACCAATTGGAGCCAAGCTGGAGACAGGAAACCCATATTACTGTTACATTGACGACAATACCGGTCAAGCAAACATCAAGAAATACAGCAGCTTGGAAAACGCGATCGTTGACGATGTAAGAATTCTTGGCAATGACGATGGCACTGGTTCACTTCAGAGAGCGGCTATTAAATTGAGAATACAGAGAAACCCAATCATTGGAGACAAGTTCTCAAGTCGGCATGGACAGAAAGGAATTTGTAGccaGAAATGGCCAATTGAGAATATGCCTTTTACAGAATCTGGCATGACTCCAGATATCATATTTAATCCACACGGCTTCCCTTCTCGTATGACAATCGGTATGATGATAGAGAGTATGGCTGGTAAATCCGCCAGTCTCAATGGACTTGCATATGATGCTACACCATTTACCTTCTCAGAGGAGGATCCTGCTATTGATTACTTTGGAAACCTCTTAAAACAATCCGGGTACAATTACTACGGCACAGAACGAATGTACAGTGGCACGGACGGCCGTGAGTTTAAAGTTGACATATTTTTTGGAGTGGTTTACTATCAGCGACTGAGACACATGGTGGCAGACAAGTATCAGGTTCGGACAACAGGCCCCATAGACATACTAACACATCAGCCAGTACAGGGTCGTAAAAGACAAGGAGGCATTCGGTTTGGTGAGATGGAGAGGGATGCGCTCCTCGCGCATGGTACCtcttttctgttgcaagatcGACTCATGAACTGCTCAGACAAAACAGTGGGTCAGGTGTGTACCAAGTGTGGCAGCATACTATCCCCTCTCCTGGACAAACCTGCCGTCGAGTTGGCAGCTGCGGCTGCGCACAGAGAACGGAAGTGGACTTGCAAAACTTGTGAAAGCAGCGAACACATTCAGCTGTTAGCCTTCCCTTACGTCTTCCGTTATCTTGTGGCCGAGTTGGCGGGCATGAATATCAAGACGTCGTTGGAAGTGAAAAGAGTTGGGACTTAA

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003184 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00562 all species →	RNA_pol_Rpb2_6	RNA polymerase Rpb2, domain 6	Domain	Interproscan
PF04560 all species →	RNA_pol_Rpb2_7	RNA polymerase Rpb2, domain 7	Domain	Interproscan
PF04565 all species →	RNA_pol_Rpb2_3	RNA polymerase Rpb2, domain 3	Domain	Interproscan
PF06883 all species →	RNA_pol_Rpa2_4	RNA polymerase I, Rpa2 specific domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007120 all species →	Domain	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Interproscan
IPR015712 all species →	Family	DNA-directed RNA polymerase, subunit 2	Interproscan
IPR007121 all species →	Conserved_site	RNA polymerase, beta subunit, conserved site	Interproscan
IPR014724 all species →	Homologous_superfamily	RNA polymerase Rpb2, OB-fold	Interproscan
IPR007641 all species →	Domain	RNA polymerase Rpb2, domain 7	Interproscan
IPR037034 all species →	Homologous_superfamily	RNA polymerase Rpb2, domain 2 superfamily	Interproscan
IPR007645 all species →	Domain	RNA polymerase Rpb2, domain 3	Interproscan
IPR037033 all species →	Homologous_superfamily	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Interproscan
IPR009674 all species →	Domain	DNA-directed RNA polymerase I subunit RPA2, domain 4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR20856 all species →	DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2	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
GO:0032549 all species →	Molecular Function	ribonucleoside binding	Interproscan
GO:0001054 all species →	Molecular Function	RNA polymerase I activity	Interproscan
GO:0005736 all species →	Cellular Component	RNA polymerase I complex	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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
K03002	RPA2, POLR1B; DNA-directed RNA polymerase I subunit RPA2	EC:2.7.7.6	Transcription machinery	ko03021	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 Platygyra sinensis 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 Platygyra sinensis, 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 →