Gene detail

Detailed information of ENSOJPP00000017941.1 in Anthopleura xanthogrammica

Genomic Location: chr11:4115826...4126678
NR annotation: XP_031574369.1, parafibromin-like [Actinia tenebrosa]
Species Anthopleura xanthogrammica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSOJPT00000020754

CAGGCATGTGGTCAGTCGGGAAGACAAGATGGCGGACCCTCTGTCTCTACTGCGTCAGTTCAACATCAACAAAAAAGAGATCCAAGAAATAGAAGATGAAGTCATATTCGACGAATTCTCCTTCCCAAAGACTGCTAAGACTAATTATGTCATCATTAAGTCGCAGCCAAAAGAGTATTATACTTTGGAATCATTGCTGTTTCTGCTGAAGAATGTTCACTTATCTCATCCAAACTACGTCCAACGTGCTGTGGGTGCAAAGATTCCAGTCGTTAGATTGCCAGATAGAAGGGCATTATTGAGCTACCTCAATGGCGAAACAGACACATCAGCAAGTATTGACAAGAGTGCTCCCTTGGAGATGCCGACACAGAGATCAACGACAGCACGCATACAAGCAGCTAAACGAGCTGGTGAAGATGCAGCTGGGGGTGAATTTAAGAAGCCCAAAGTTGAGACTGCAGAAGTTATCTTGGACAAGagAAAACTGGAAGCTCGTCTTGAAGGTCACAAAGAAGTTACTGTAACAACAGACCAGATGAGGTCATTGAGTGAAGCCATGACCAAAGAGAAGATTGCTGCTATTAAAGCCAAGCGTCTCGCCAAGAAGAAGACAACAATCCGTGTGGACGATGAGCTGGAACCAGATTTACTGAAACAACGTAGTTTTGTAGATGCCGAAGTAGATGTAACGAGGGATATTGTCAGTAGAGAAAGACTTCTCAGGACGCGTACCAGTGTTCTACAAAGCTCTGGCAAGCATTTTGTCAAGAATATTTTAGCCATACTTCAGTCTGTCAAAGCTAGAGAAGAAGGCAAACACAAACAGAATCAACCAGCAAATGCATCAGCATCTGTGGATTCTGGCAAGAGAAAACCTGCTGCTCCTGTGGCCTACAACAGATATGATCAGGAACGATTCAGAGGAAAAGAAGAAACCGAAGGATTTAAGATTGATACTGCTGGAACATACCATGGATTGAGTTTAGAGCACGTCAAGGAAGGAACTCACAGGCCAGTAAAAAGGCCAGCACCAAGCCCATCACCTCACACCCAGCCATCAAAGGCTCTTAGACCAATTCAACCGAAACCAGCTAAACGAGAATCCAGAACACCTATCATCATAGTGCCTGCTGGAACAACATCGCTCATCACACTATACAATGCTAAAGATCTATTACAAGACTTTAAGTTCGTTACATCAGACGAGAAGAAACGGTCAGGCACACGAAGAGAAAACGAGGTTCTCCTTCAAAGACGTAAAGAAGTGGTTCAAAACCAGCACGCGGGCTCTACGACCACGACAGTCACGGTACCATACCGTGTAGTGGACAATGTATCACGTCTGCAACAGAATGACTGGAATCGTGTAGTTGCAGTGTTTGTACAGGGACCTACATGGCAGTTCAAAGGATGGCCATGGTTGCTGGCTGATGGCTCGCCCGTTGATATATTTACTAAGATCAAAGGCTTTCACCTCAAGTTCGAAGACGTCAAGACTGAACCAAATGTCCAGAAATGGGACGTCCAAGTTCTAACGATCAATCGTAACACCAGGCATTTCGACAAGGCGTCAATCAACACGTTTTGGACCACGATGGACAAATTCATGGTCAAAAACAAGCCACAACTGAGGTTCTGATGGACAAAAACACGGCAAATAAGACAGAAATGTTTGGTCTATTTTCATCTTTCcaccaaatattttaaatggTCCGAATCTTTCCAATGTTAATACttaaacaatataaatacTTTATCCTATCTCAGATGGTTTTTATAGTCCAATGAAAAATCATGAGGCATAAGttatgacgtatttccgggtcagAAAGCGCTACACGACgacaaaatgaaagaaatattcCACAATTTTATTTCTAGATGTAAGAATTTCATTGGCATATGAACAGTACTTAGAAATCTGGGCTGAATCTTCCAAACGAAGCGGCTGATATGAagtaaataaatctttatgAACAACTTACTTTTTTTCAGGATTTCCTATATTGTAGTGTAGAATAAAGATCTTGTACAAATACAGAAATCTTTTGAAATTCTGTTTTTATCATTGGGTTAGTCCATGTAGTCATTTCTTTGTACGTGTCTATTTTTTAATCACCCTCCTAGCTCCTTTCCATCCTCTTGGTGTGCGAGGTTGGGGGACCAGAAAGACCTAGGAGCACCAAAACATCCCAAGACGTCTACCGGTTTTGACTTGGAAGAGCCGTGTAACCATTTCTTTCTAGGTGTCCAtcttttaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6P1J9	Parafibromin OS=Homo sapiens OX=9606 GN=CDC73 PE=1 SV=1
Q8JZM7	Parafibromin OS=Mus musculus OX=10090 GN=Cdc73 PE=1 SV=1
Q4V8C8	Parafibromin OS=Rattus norvegicus OX=10116 GN=Cdc73 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005327 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16050 all species →	CDC73_N	Paf1 complex subunit CDC73 N-terminal	Family	Interproscan
PF05179 all species →	CDC73_C	RNA pol II accessory factor, Cdc73 family, C-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038103 all species →	Homologous_superfamily	Cell division control protein 73, C-terminal domain superfamily	Interproscan
IPR032041 all species →	Domain	Paf1 complex subunit Cdc73, N-terminal domain	Interproscan
IPR007852 all species →	Family	Cdc73/Parafibromin	Interproscan
IPR031336 all species →	Domain	Cell division control protein 73, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12466 all species →	CDC73 DOMAIN PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000993 all species →	Molecular Function	RNA polymerase II complex binding	Interproscan
GO:0006368 all species →	Biological Process	transcription elongation by RNA polymerase II	Interproscan
GO:0016593 all species →	Cellular Component	Cdc73/Paf1 complex	Interproscan
GO:0032968 all species →	Biological Process	positive regulation of transcription elongation by RNA polymerase II	Interproscan
GO:0034402 all species →	Biological Process	obsolete recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex	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
K15175	CDC73; parafibromin	-	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 Anthopleura xanthogrammica 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 Anthopleura xanthogrammica, 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 →