Gene detail

Detailed information of KAL9956041.1 in Oculina patagonica

Genomic Location: chr12:13201295...13220951
NR annotation: XP_020617944.1, mediator of RNA polymerase II transcription subunit 25-like isoform X3 [Orbicella faveolata]
Species Oculina patagonica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ACROYT_G037460

ATGGTGGCTGCTGGTGATTTGTACGAAAACGATGTTGTGTTCGTTGTTGAGGGCACTGCAAACTTGCTGCTGGACTTTGAAAACCTAAAGAAATCCTACATAGAACCCGCAATACATTATTTCAATGGAGAGATTCCTGTGGACTCTGAATACAGCTTTGGAGACGAGTATGGACCAAACCAGTATGGTCTGGTGGTGTATGGAACAATAGGCCACACTCCTGAGCCAGCTGTACAGTATGTCAAAGAAACACGCAATGCTAAACAGATGCTACAATTCCTAGATGAAGTGAGATTTGAGGGTGGAGGGGGTGAGGAGTGCAGTTTATTAGCTGAAGCTCTAAGTATTGCTTTGCAGATCTTTGATGAAAGAACTCTTCAGAGGGGCCAAGGTTATAAAAATATCGTCCGTAAAAGCTGTATGGTGGTGTGCAACTCACCCCCATTTGGTTTGCCAAGCCGTGAGTGTGCAGATGATTACTACGACAAAACTGTTGAACAACTTGCTGAAGAAATGGGCCAAAAGAAAGGAATTCATCTCTCCATTATTTCACCTAGAAAAATTCCTGCACTTCAAAGGGCATTTGAAAGGTCTTTGATAGTTGACAGTAAAAGTATTTTATCAAAAGATTACTCCAAAGATCCTAACCATCTGGTGTGCATACAGGGTCTGGATTTGCCAGTTACTCGCAGCAATGATTCACAAGCTGAAGTATCAAAGAATGGGGCACACATAACTGATACTAACATGAAGTCTGTAGCGACACCTTCCCAGATGACTGCCAGTGTGAAAGAAAGTCCAGAGAAACCAAAGAAACAAAAGACAATGCCTCGTCAACCTTCATTGCCTGAAACCAAACTGCCACAACAACCAAATGTTAGCATGCAGTTAGGTATTGGATCAACTCCTAATATGCAGGTGTCGCAGATGCCACCAGATAGTATGATGGTAAACACACCTCAAGCAACACCAGCTGCAGGTTTGAACAACAATCCAGCAGCACAGCAAAAAGCTAAAGAAATCTTGAGAATTGCATTAGGGCAATCCTTCAGGAACCCAGCTCCCACTGGTGGACAGCCTCAGCCCAATTCAATGCAGGATGGTGCATCAGGAAATTGGGCACAGACTCCGGGCAACCAAGCACCTAGACCAGGCCCTGTGACTGGAGCTACACCAACTGTAAGCTCAGAAAATCCTCAAGTAGCTCCCAGTCAGAGAGCTCTTGCCTGGACAGGTCATTTGGAATGGCAGGATACTATTCGTGACCCTAATGGCCCTCAGCAGAGAATAACACGTTCTTTGGCTTGCCATGCATCAGTTGTTTCTGGAGATACTCTCAAAGCTAACTGGCCTCCAAAGCTTATCATGCAACTCATCCCACAGAATCTGCTGTCCACATTAGGACCCCTGCTACAGAACTCCAAGACAGTGGCATTCCATTTTGCTCCTAATGATCAAGAATCTTTGAGAGCTCTTTACAGAGTAATGGCATCCAATGGAGTCAAGTTTGCAGGCTGTGTTCATTTCCCACCTGTTCCACAGTGTGATGTTAAAGTTCTTCTCTTGATTTTTAGTCCTAAGAAACGTGCATTTGTTGGATTAATCCCTCAAGAGCAGACAAACTTTGTGGAGGGAATAAGGAGTGTTGTGCAAAAACACAAAATGGAGCAACTCGCTAAGGTTAGGCTTCATCAACAACGTATGCTTCAGCTCCAACAGCAACAACAACAACTGAGACAGCAACCACAACAGCAGCCTCAACAACAGCCCAACTTTGTTGCAGCTGCCGCTGCTGCAGCAGCTGGTATGGCACAAGGCCAGTTTCCACAGCAACAGTCACAAGTTTCCCAGCAGCCTCTGATAAATTCTGGAGGAAATGCACTGATGACCAGTGCAACACAAGGCTTAGGACAAAACCCAGAGGGATTGGTGACTAGTGCTCAGAGCTCTGTGCCCCCCAATATGGGATTAACATTCAGTGGAGTGAACACTGGGAACCACAATATGCCTGTTTTGTCCATGGATCAACCGGACAATGCTGCTCTACAATATCAAGCGTTCCAAGAGTTACAGCTCAAGCAACAACAGAAGCTATTACAGCAACAACAACAACTACAGCAGCAGCAACAACAACAGCAGCAGCAGCAGCAGACACAACAGCTGACGCCGCAACAGATACTAGCACGGACAAGACAATTTCAGCAGCTTCAACAGCAGCAGCAACAACAACAGCAGCAGCCACAGCAACAACAAACCTTTCAGACTGCACAGGATCCACAGGTTCAACAGATGCAGACAAGCCAGGGAATATCGTCACAGCTTCGTCACCTCCTTCAGGCAAACCAGGCTTCAGCCCAGCAACAAGGGCTGGCAGGTGCACAGCAGCAAGGAATGACTCAACAGCAGTGGCAGCTACTGCAGCTACAGCAGCAGCAGCGGTCTCAGGCGGGTGTTCAGATGCCGCTTGGCCAGGTGCAGATGTCGCAAGCACAGATGGCTCAGACCCAGTCCCCCATGTCTCAAGGTCAGGTATCGCAGGCTCAGATGCAAGTTCAGCAGCAGCAGCAGTTATCGCAGTCTCAGTCCAGTTTTCTCCCGGACAACATGAGCTTACTCGACATACTGCCATAG

Transcript

rna-ACROYT_G037460.t0

GGAAGAACGCAGCGAGCTCGGGATGTAGAATTTTATTTGGTATTCTTTCCGCTTTCGGAGGTTTGCTTCGCGAAGTTGTTGTGGTATCATCTGGCTAAAAATATCACTTTGAATCATAATCGGGGATCCCCCTCAAAAAGGATGGAGTATATAGATGAGGGTTGATCGACTTCCCGTTAATCTTTAGAGAGGAACTCGTTGATAATGGTGGCTGCTGGTGATTTGTACGAAAACGATGTTGTGTTCGTTGTTGAGGGCACTGCAAACTTGCTGCTGGACTTTGAAAACCTAAAGAAATCCTACATAGAACCCGCAATACATTATTTCAATGGAGAGATTCCTGTGGACTCTGAATACAGCTTTGGAGACGAGTATGGACCAAACCAGTATGGTCTGGTGGTGTATGGAACAATAGGCCACACTCCTGAGCCAGCTGTACAGTATGTCAAAGAAACACGCAATGCTAAACAGATGCTACAATTCCTAGATGAAGTGAGATTTGAGGGTGGAGGGGGTGAGGAGTGCAGTTTATTAGCTGAAGCTCTAAGTATTGCTTTGCAGATCTTTGATGAAAGAACTCTTCAGAGGGGCCAAGGTTATAAAAATATCGTCCGTAAAAGCTGTATGGTGGTGTGCAACTCACCCCCATTTGGTTTGCCAAGCCGTGAGTGTGCAGATGATTACTACGACAAAACTGTTGAACAACTTGCTGAAGAAATGGGCCAAAAGAAAGGAATTCATCTCTCCATTATTTCACCTAGAAAAATTCCTGCACTTCAAAGGGCATTTGAAAGGTCTTTGATAGTTGACAGTAAAAGTATTTTATCAAAAGATTACTCCAAAGATCCTAACCATCTGGTGTGCATACAGGGTCTGGATTTGCCAGTTACTCGCAGCAATGATTCACAAGCTGAAGTATCAAAGAATGGGGCACACATAACTGATACTAACATGAAGTCTGTAGCGACACCTTCCCAGATGACTGCCAGTGTGAAAGAAAGTCCAGAGAAACCAAAGAAACAAAAGACAATGCCTCGTCAACCTTCATTGCCTGAAACCAAACTGCCACAACAACCAAATGTTAGCATGCAGTTAGGTATTGGATCAACTCCTAATATGCAGGTGTCGCAGATGCCACCAGATAGTATGATGGTAAACACACCTCAAGCAACACCAGCTGCAGGTTTGAACAACAATCCAGCAGCACAGCAAAAAGCTAAAGAAATCTTGAGAATTGCATTAGGGCAATCCTTCAGGAACCCAGCTCCCACTGGTGGACAGCCTCAGCCCAATTCAATGCAGGATGGTGCATCAGGAAATTGGGCACAGACTCCGGGCAACCAAGCACCTAGACCAGGCCCTGTGACTGGAGCTACACCAACTGTAAGCTCAGAAAATCCTCAAGTAGCTCCCAGTCAGAGAGCTCTTGCCTGGACAGGTCATTTGGAATGGCAGGATACTATTCGTGACCCTAATGGCCCTCAGCAGAGAATAACACGTTCTTTGGCTTGCCATGCATCAGTTGTTTCTGGAGATACTCTCAAAGCTAACTGGCCTCCAAAGCTTATCATGCAACTCATCCCACAGAATCTGCTGTCCACATTAGGACCCCTGCTACAGAACTCCAAGACAGTGGCATTCCATTTTGCTCCTAATGATCAAGAATCTTTGAGAGCTCTTTACAGAGTAATGGCATCCAATGGAGTCAAGTTTGCAGGCTGTGTTCATTTCCCACCTGTTCCACAGTGTGATGTTAAAGTTCTTCTCTTGATTTTTAGTCCTAAGAAACGTGCATTTGTTGGATTAATCCCTCAAGAGCAGACAAACTTTGTGGAGGGAATAAGGAGTGTTGTGCAAAAACACAAAATGGAGCAACTCGCTAAGGTTAGGCTTCATCAACAACGTATGCTTCAGCtccaacagcaacaacaacaactgagACAGCAACCACAACAGCAGCCTCAACAACAGCCCAACTTTGTTGCAGCTGCCGCTGCTGCAGCAGCTGGTATGGCACAAGGCCAGTTTCCACAGCAACAGTCACAAGTTTCCCAGCAGCCTCTGATAAATTCTGGAGGAAATGCACTGATGACCAGTGCAACACAAGGCTTAGGACAAAACCCAGAGGGATTGGTGACTAGTGCTCAGAGCTCTGTGCCCCCCAATATGGGATTAACATTCAGTGGAGTGAACACTGGGAACCACAATATGCCTGTTTTGTCCATGGATCAACCGGACAATGCTGCTCTACAATATCAAGCGTTCCAAGAGTTACAGCTCAAGCAACAACAGAAGCTattacagcaacaacaacaactacagcagcagcaacaacaacagcagcagcagcagcagacACAACAGCTGACGCCGCAACAGATACTAGCACGGACAAGACAATTTCAGCAGCttcaacagcagcagcaacaacaacagcagcagccaCAGCAACAACAAACCTTTCAGACTGCACAGGATCCACAGGTTCAACAGATGCAGACAAGCCAGGGAATATCGTCACAGCTTCGTCACCTCCTTCAGGCAAACCAGGCTTCAGCCCAGCAACAAGGGCTGGCAGGTGCACAGCAGCAAGGAATGACTCAACAGCAGTGGCAGCTACTGCAGCTACAGCAGCAGCAGCGGTCTCAGGCGGGTGTTCAGATGCCGCTTGGCCAGGTGCAGATGTCGCAAGCACAGATGGCTCAGACCCAGTCCCCCATGTCTCAAGGTCAGGTATCGCAGGCTCAGATGCAAGttcagcagcagcagcagttaTCGCAGTCTCAGTCCAGTTTTCTCCCGGACAACATGAGCTTACTCGACATACTGCCATAGTGGAACTATGTTTTATGTAAAACCTAACGTATTGTACACTTGTGCCTGGTTTGACATCATCTGAAATGCAACAGGGAACCCTGCTTTATTTATCTTTTGCACAGAAGAAAAACgtcaattttttgtttgtcgTACCTTGTTAAGTATACTTGACAGAAGTAACGTGTAAAACCTTTTGTACTTGTAAAAGACCACGGTCGTAATTTCACGAGACCGTTTTGCATGAAATGTCCGCGGTTAACTAGAAACAAAAAAGGATAAGTTtacgtaaaaataaacaataacgTTCCATATGCATACAGTTGTAACTAGCATTAAAATGTTTTATAGTCTTGGAGGATTAAATTATTgagataaaatatataaaactttgCTAGGGTTTTTAGGTGTTGATCCAAGATCAATAAGTATAAACGTTGTCTATGACATCATAGTGATCACTGGAAACGTTTTCAGAAGTCAAGAAATCAAGTCAAACTTGTGAAGCATCTTAACAATGGTTTTTCCgataacttttgaaagaaatgtaaatgtgcCAAGTTGTTTGTTCAGACGAGATAAAAGCTTTTCACGTGAGGCACGGGACACAGCCAGGATAGAAGAAAAACACTAGCTTTATGTCGCCTAAAGGTTCGTTTGGAAAGTTATCGGAAATGACCTCCTCAAAGATACAtgttacatgtaatttgttCAGATAATTTTAGTAACAATATCTGTTTAGTCTTTCAAGCGTCAGTCTTTAAATAGATAGAGTACTGTTAGACCTTTCAAgtgtaaaaattgcaaagcAGAATAAAGTTCAACTGTATTAAATAGCCA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6GP15	Mediator of RNA polymerase II transcription subunit 25 OS=Xenopus laevis OX=8355 GN=med25 PE=2 SV=1
A4IHD9	Mediator of RNA polymerase II transcription subunit 25 OS=Xenopus tropicalis OX=8364 GN=med25 PE=2 SV=1
Q71SY5	Mediator of RNA polymerase II transcription subunit 25 OS=Homo sapiens OX=9606 GN=MED25 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003925 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11232 all species →	Med25	Mediator complex subunit 25 PTOV activation and synapsin 2	Domain	Interproscan
PF11265 all species →	Med25_VWA	Mediator complex subunit 25 von Willebrand factor type A	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan
IPR021394 all species →	Domain	Mediator complex, subunit Med25, PTOV domain	Interproscan
IPR038196 all species →	Homologous_superfamily	Mediator complex subunit 25, PTOV domain superfamily	Interproscan
IPR021419 all species →	Domain	Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12433 all species →	MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 25	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0016592 all species →	Cellular Component	mediator complex	Interproscan
GO:0045944 all species →	Biological Process	positive regulation of transcription by RNA polymerase II	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
K15168	MED25; mediator of RNA polymerase II transcription subunit 25	-	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 Oculina patagonica 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 Oculina patagonica, 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.

Dataset	Tissue / stage	Cells	Cell types	This gene	Marker of
OPATA_whole_adult	Whole adults · Adult tissues/organs	21,775	31	not in this dataset	–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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 →