Gene detail

Detailed information of ENSDJXP00000039910.1 in Hydractinia echinata

Genomic Location: JASGCC010000149.1:242304...253623
NR annotation: XP_012558903.1, general transcription factor IIF subunit 1 isoform X2 [Hydra vulgaris]
Species Hydractinia echinata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSDJXT00000045514

gtttcaaaTGGGAATTTGgggtgaaaaaaaatgaatgggTTTTAACACAGGACTTACAGTTGTAATTATGTAACTGTTACTTGCAATCAAACATAACTTTCAGGTCTATAGATATTAGTTCTGAAATGCTTACTGAGAAGAAACTCTAAGCCACTTTTACGATGTTTCCTTGTCAAACGTTAATGAAacgataaaattttatatataaataataaagatgCAAAAAAGTGGACCACCGATGATCGGCAAAGTGACAGCCAAACAAGAACAGTATACAGAATACAAATTGAGAGTACCAAAAAATTTAGTCAAGCGATACAATGTGATGAAACTGAACTCACCAAGACCAATAAAATTGGGTGACATTAAAGAGGCCAACATGGTTCGTAAAACTAAAAAGCAAGTTTACGTGGAAGAAGAGGCAGCATCCATGCCAACATACGGTGCTGGCAGTGTATACAATTACGAGAGAAAGGAAGAAGCTCGAAAAAAACGCAGAGGGTACATTACGAGAGAAATCAATCTAGATGATCTTCCTTATGCGCTTCGGTTGGGTGGAAAGGGAGGTAAAAGATACACTGGACGAAAAGAACCGATCCTGGAACACTCTGCTTACTACATTCTAACACAATGTCCGGATGGCGTGTTTGAGGCAGTACCTGTACAAGCGTGGTACAATTTCTTACCAGATATCGACTATTCTACGCTTACTTCAGACGAAGTTGAGCAAGAATTTTCTAAACGTGATCGTACGTTAAGTTATTTTACAACGAAATATCAGATAGGTGGGGAAGAGCAAGATGAGATTAGTAAAGTGAGAAGAAAAGATGACGACCACAATTTGATTATCCACGATGATGAGATCGATGAAGAAGatcaagaagaagaaaatgaagaGGAGAACGAAGAGGAGaccgaaaaaaagaaaaAGAAAGTATCCAAAAAAGAGAAGAATATATTTcgtggtaaaaataaaaaagaaggaaatgattcggatgaagaagaagaacttgGAAACTTCGAATCAAAAGAAGTTGATTATATGTCGGAATCTTCATCAgaGGATGAGTTGATTGAGATGGACGATGAACCCGatccagaaaaagaaaaatcggGAAAAGCTAAAGACGACTTGAACATATTTTCCGACTCTGAAAATGACGATGAGGAGGAGAGCGATTTAAATGAGGCTGGCAAGCAGTTGAAATCTATGTTAAAGAAGGAATCTGGTATTGGAGGGAGTTCtgatgaagaagaagaggaggaagaagaagatgaagatATTGATAATGAATTTTCAAAGTCAGCTGTTTTTATGCAAGGTAAAGACGGTAAAAAGAAGAAAGGAAAATCAGGCAGCAATTCTGGTTCGAAACCCGGAAGTAGATCATCAACTCCTGTGCAAAGTGACCAATCCACTGATACGTTGTCGCAGGCTGCCAAATCTTTAAAAGAAGGTAAAGCAGGCTCAAAGCGAAGTATGGATCGTTCATCGCCCAGTCCACAatccaaaaaacaaaaacttggaTCCATTGTTACCGGTAGCCGAAACAGTCCTAGTGGATCTCGTTCTGCAACACCGTCTGATGGAGGAAGTAAGACTGGCTCCAAGCGAGGTATGGATCGTTCATCACCCAGTCCACAAGGcaagaaaacaacaacttggTTCCATTGTTACCGGTAgcagaaacagtccattgttaacggATTCAAGAAGTGGATCTCGATCTGGAACACCCCTCCGATGGAGGGAATACGATAACTGAGGAGGCTATACGAAGATATCTTACACATAAGCCCATGACCACTACAGACTTAATGAgaaagtttaaattaaaaaagacaGGATAAGTTAAAGAACAAACTGTGAATGCTATGGaacaattttaaagaaaaatacaaCCACATCAAGAAAAGATTGATGGGAAGTTATATTTgtcaatcaaaacaaaaagatagagaatttcaaggtttttttttgGTGAAGACACGGCATATATGGAAATACACAAAAATGTATCTCGCACGCTGTATTTCCTTTTGGTTGAGTTGGAAATTATGTCAGAAAGAATTCTATTTCACGCATGCGCGTTTTTTAACCTGTTTACAACTGACCGTGGTTCATATGAACAATGCGGTGATTCACGATTCGGAAAGTGCGCGCTAAACGTTAATCCAACGTTGCGCTACGCTACGCTACGTTACGttttgttaaatatttcatAGCATAATACATCGATTTTTTGGACAATAGAGGTGTTTTAGACTAGTTTGTTGCTCACAGGAGCGATTGTGAGTAAATTGTGGGTAAAATCTAATCAACGAATGTTTTAGcgtgcaattttttatttgcgAATCGCCCgttataattattttgttataatGTCTTTACAGCATCTGAAACGTAATTGGTTCTTTGATAAGATTTGAACATGTGCAGAAGGAGGAAAAATATTGTCTTAAGTGAATTATTTTTAGCAggaaataaattgtcgcgaatATGGCGAGGTTTTGTCAATTtggcgaaaattagttcccgcgaaaaaataattcatttcaatttaatatttttcctCCTTCTGCACATGTTCAAAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q04870	General transcription factor IIF subunit 1 OS=Xenopus laevis OX=8355 GN=gtf2f1 PE=2 SV=1
Q3THK3	General transcription factor IIF subunit 1 OS=Mus musculus OX=10090 GN=Gtf2f1 PE=1 SV=2
Q6AY96	General transcription factor IIF subunit 1 OS=Rattus norvegicus OX=10116 GN=Gtf2f1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005721 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05793 all species →	TFIIF_alpha	Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008851 all species →	Family	Transcription initiation factor IIF, alpha subunit	Interproscan
IPR011039 all species →	Homologous_superfamily	Transcription Factor IIF, Rap30/Rap74, interaction	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13011 all species →	TFIIF-ALPHA	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006367 all species →	Biological Process	transcription initiation at RNA polymerase II promoter	Interproscan
GO:0032968 all species →	Biological Process	positive regulation of transcription elongation by RNA polymerase II	Interproscan
GO:0001096 all species →	Molecular Function	TFIIF-class transcription factor complex binding	Interproscan
GO:0005674 all species →	Cellular Component	transcription factor TFIIF complex	Interproscan
GO:0016251 all species →	Molecular Function	RNA polymerase II general transcription initiation factor activity	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 ENSDJXP00000039910.1.

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 Hydractinia echinata 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 Hydractinia echinata, 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 →