Gene detail

Detailed information of BRAKERXEIP00000042297.1 in Muricea muricata

Genomic Location: chr3:1210949...1226259
NR annotation: XP_028397561.1, LOW QUALITY PROTEIN: transcription initiation factor TFIID subunit 1-like [Dendronephthya gigantea]
Species Muricea muricata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERXEIT00000042297

ATGGCGACCGAAGAAGGCGAAGAAAAAGATTCAGACTGGAGTTTAACTGGATTTCTCTTTGGAAACATAAATGAAAAAGGCGAACTAGAAGATGAATCAATATTAGATGAGGAATCTCGCCGTCATTTGTCTCGTTTGGAAAGTCTTGGTGGATTAGGAAGCTTGGTGAAGGATATTTCAAGTTTAGAAGAAAAATCTGAAAGAAGTCATGTGCTGGACCATGTCGGAgATAGTGTATCAAAGGCCTATAATGCTGCAGATTTTAGTGAAATAAATGAATTGGCTGATGATGAAGAAGCAAATTATAAGCGAGGTTTAACATTTCTCTCAGGAAAGGGTAAAGTTTCATCAAGATCAAATAGAGATGATGACGATGATTATGAATGCAGTGAAACAGATCCACGTAAAGATGCACTCACAAAAGCAGAGCAAGATAGACTGGCAATGCCTCCACCAATAATGGGTAACCATGTATCAGATAGCGGAGCAACAAAACAAGATGGTGTAACTGATACTTCATTTCTTCCTCAAACGTCTGATGGTAAAACAGTTCTTGATCTATTTCCTGAGTTCCGACCAGGAAAAGTGTTGCGATTTTCTCGTCTCTTTTGGCCAGCGAAACCATCATCATTACCTCAGCTGTGGAGGAATGCCAAGAAAAGAcggaagaaaaagaaaagacaagaGGATCCTACAACGCCGATATCATCTTCATTTAAGATTCATGATGAATATATGTCAGATGACGAGGAGAGATTAATGCGACCAAtagaaaatgataatcaaacaAATAAATCTGCTCTACAATCACGTGATGGTATTGataaagaagaagaaaagaaagtGTGTGCATGGCGACATGGACCTGCGGCTTTGTGGTATGAAATGCTCGGAGTTAATGAAGACGGAACAAATTTGGACTATGGTTTCAAGTTGAAGGAAGATACTGACGTTAAAGAAGAAGAGTTGACgattaaagaaattgaagaagAAAGAAAATTTCCTTCAGATGATTGTTTTCATTTGGTTGCGATCAAGAGATGGGAAGATGACATCATCTGGTCTGCTCAGGATGTAAAACTCAACCCACTAGCTGAAGGCATTGCGGGCTGGATACCTTCAGCAAACATCAGAACAACGTTAGCTTATGCCAACCAGCATACATCAGGATCTAAACTTTCTGGATTGGAGCAAAGTATCAATAAAACAAAAGCAGCTATAAAAGCGAACCATGCTGCATTGACagaaaatgtaaaagaaaataaacCATGGTATTCTATATTTCCTGTCGATAACCAAGAACTGATTTATGGAAAGTGGGAAGACAAGATTATTTGGGATTCCGAGGCCATGACAAATATTCCCGAGCCAGAAATCATGGAACTGGATCCTAATGATGAAAACCTCATCCTTGGAATTCCGGAAGACGTTGTTGTAAGCACTGGTAAAGAACAAGAACCAACACGACGACGTGAACCAAAGAATAAATCAAAGTTATTGTTTGGAAAATCAAAAACGGAAGACGAAGACGAGGAAATGGCATCACTTGATGAAACCCCTAAAGATCCGTTCAATAtatcaaatgataaatattACAATCCCAAACACACCACGGCTGAGAGTAGCCTTCAAGCTACAATGGGTACAAATCGGATACAGCATTCCACGCCAGCCATGGAGTTGCAACGTCCATTCTTTCCTACATTTAACTCAAAAGAAAGTTTAAGACATTTTCATCGTCCTCTGTTGAAACGAGTTACTAACGGAAAGTTGGCAGCTCCAGGACCACATCCGGTATCTGGTCTGTTAAAACACATCAAGAAAAAAGCCAAGGAACGACAAAAAGAACGTCTTGCTTCAGGCGGTGGAGAAGTATTCTTCATGCGCGATGTCACTGATCTAACAGGAATGGATGGTGATCTAATATTAGCCGAATATTGTGAAGAATATCCTCCGTTGATCATGGCAGTTGGCATGAATACCAGAATTATTAACTACTATAAAAGGAAACATGGGAAAGATGAAGGTGCTCCTAATTTTGAATATGGAGAAACATTGTACATCCACCAAACATCGCCATTCTTAGGACAACTCAAGTCTGGACAGTCATTACAGgcattggaaaacaatttatACCGAGCTCCTATTTATGAACATGCAATGCCAACCACGGATTTTGTTATCATAAAAACAAACAACAGTTATTATATACGCGAGgtaaaaacaatgttttgtgTTGGTCAAGAATGCCCAAAATTTGAAGTTCCCGGGCCGAACTCGAAGAAAGCAAACAATCACGCTCGTGATTTTCTACAGGTATTTATCTACAGATTATTTTGGAAAAGTCCAGACAACCCAAGACGTATTAAGATGGATGATATCAAGAAAGCGTTTCCCCATCATTCTGAAAGCAGTATAAGAAAACGTCTAAAACTATGTGCAGATTTTAAAAGAACCGGGGTTGATTGTAACTGGTGGGTTCTTAAAAATGATTTCCGTCTACCGTTTGAAGATGAAATGAGAGCTTTAGTTACTCCAGAACAATGTTGTGCTTATCTCAGTATGCAAGCAGCCGAACAAAGATTAAAGGATGCAGGTTATGGTGAGAAAAACATGTGTGCGAGTGACGACGATAATGAAGAGGAAAACCAAAAGATAGACGACGAGGTTCGAACTGCACCGTGGAACACAACACGTGCATTTATATCTGCCATGCGAGGCAAGTGTCAACTAGCGGTAAGCGGTCCAGCTGATCCAACTGGATGTGGGGAAGGATTTTCATACGTCAGAGTTCCAAATAAACCAATTGCGTCAAAGGATGACAACAATGCTCAGAATCCATCTgtaagaaaacaaaaaacagtGACAGGAACCGACGCAGATTTACGACGTTTGTCATTGAAAGATGCCAGAAAAGTTCTCAGAAACTTTGGAATACCTGAAGAGGAGATAAAGAAGCTATCAAGATGGGAGGTCATTGATGTTGTACGAACAAGGTCAACCCAAGCTGCAAAATCTGGAGAAGAACGTATGAGTAAATTTGCAAGAGGATCAAGGTTTTCTATTGCTGAACATCAAGAAAGATATAAGGAAGATTGTCAGAGGATATTTGAACTGCAAAACAAGGTGTTGTCTTCGACTGCAGTTCTCTCAACTGACGAAGAAAGTAGTAGTGATGAAGACAGTGATTATGATGAGTTAGGGAAGAATCTGGAGAGCATGTTGTCCAATAAGAAATCATCTACACAGTTAAGTCACGAACAAGAAGAAGCTGAAAGACTAGAACTTCAACGACTGTTAAACCAAGACAATAAAGATAATaatGATCAAAAGGGATCTTCAGGTACGTCACTTTTACCCATAATGCTAGAGattatatcttttatttatttttttaacgtGGGGGATTTCTCGTGTTCCGGATGTACGAGGTTAATTGCACAAGACTGA

Transcript

BRAKERXEIT00000042297

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q60544	Transcription initiation factor TFIID subunit 1 OS=Mesocricetus auratus OX=10036 GN=TAF1 PE=2 SV=1
P21675	Transcription initiation factor TFIID subunit 1 OS=Homo sapiens OX=9606 GN=TAF1 PE=1 SV=3
Q80UV9	Transcription initiation factor TFIID subunit 1 OS=Mus musculus OX=10090 GN=Taf1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002607 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09247 all species →	TBP-binding	TATA box-binding protein binding	Domain	Interproscan
PF12157 all species →	DUF3591	Protein of unknown function (DUF3591)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036741 all species →	Homologous_superfamily	TAFII-230 TBP-binding domain superfamily	Interproscan
IPR009067 all species →	Domain	TAFII-230 TBP-binding	Interproscan
IPR040240 all species →	Family	Transcription initiation factor TFIID subunit 1	Interproscan
IPR022591 all species →	Domain	Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13900 all species →	TRANSCRIPTION INITIATION FACTOR TFIID	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004402 all species →	Molecular Function	histone acetyltransferase activity	Interproscan
GO:0005669 all species →	Cellular Component	transcription factor TFIID complex	Interproscan
GO:0006366 all species →	Biological Process	transcription by RNA polymerase II	Interproscan
GO:0016251 all species →	Molecular Function	RNA polymerase II general transcription initiation factor activity	Interproscan
GO:0017025 all species →	Molecular Function	TBP-class protein binding	Interproscan
GO:0051123 all species →	Biological Process	RNA polymerase II preinitiation complex assembly	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
K03125	TAF1; transcription initiation factor TFIID subunit 1	EC:2.3.1.48 EC:2.7.11.1	Chromosome and associated proteins	ko03036	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 Muricea muricata 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 Muricea muricata, 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 →