Gene detail

Detailed information of PFX34208.1 in Stylophora pistillata

Genomic Location: Spis.scaffold6:238514...256495
NR annotation: no NCBI-NR hit recorded
Species Stylophora pistillata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

CNOT4

ATGCAAGCTTCCGATGCAGAGTGCCCGTTGTGCATGGAACAGTTGGAAATTGACGACGTCAATTTCTTCCCTTGCACTTGTGGATATCAGATCTGCAGGTTTTGCTGGCATCGTATTAGAACAGATGAGAATGGTTTATGTCCTGCTTGTAGGAAGCCCTACAGTGAAGATCCTGCAGTTTATACCCCCCTATCACAAGACGAAATACAGAGAATTCTGAAAGAGAGGAAACAGAAAGATGTACAGAGAAAACAGAAAGTAACTGAGAACAGAAAACATTTAGCAAATGTGAGAGTTGTACAGAAAAATTTGGTATTCGTAGTTGGATTAACTCAAAGATTAGCAGATCCTGAGCTTCTTAAAAGACCAGAGTACTTTAGCAAGTTTGGGAAAATACACAAAATTGTTGTGAATAACAGTACAAATTATGCAGGACCCCAGGGTCCCAGTGCGAGTGCTTACATTACATATGTGAAAGAAGAGGATGCAATTAAAGCGATAATAGCCGTGTGTAACACTCATCTTGATGGGAGAACACTAAAGGCATCTCTGGGGACAACAAAATATTGTAGTTACTTTCTTAGAAACATACCCTGTCCTAAAATGGATTGTATGTATCTTCATGAGTTAGGTGATGGAGCAGGAAGCTTTACAAAGGATGAAATGCAGGCAGGAAAACATCAAGAATATGAACAGCAGTTGATTGCTTTTTATTCGAAGAAAATGGGTCTTAGCAATGATAAGGATAAAAATGAAGAGTGGCCAGTTGAAGATGGTGGTGAAAACAGAGTATCCCCTCATCTTCCTTCAGGAGGAGCTTGGGCTGGCAAAGATGAGGACGAAGAAGGAGTTACCTGTCAAAATATTTCAGAGAATGAAGATAGTTCAGTTCGAGATAGAAAGGTGGAGGACTGGGAGGAATTGTGTCTCCCATCTGCTACTACAACTACAACAGAACATAAGCCATCCGATACCATAAGACAAGAACAACCAGCAAACCCTCCACAGTCAACGTACAGCAATGCTGGTTGGGGAAATACAGAAAGTGCTGGACGTGCTTTAGATACCTCTGGTCTGTTCTCTGCTGATCTCTGCAGTGGTCTGGGCCTTTCTAACTTACATCTGAAAGTTGATGGTGAAGATGATTTAGGTTTTGATCCTTGGAATGAGTGCAGTAAAGGTTTGGCAGATCTTCTTCAAGAGGAAAACAAAACAACAGTGCCTGGACAGACACATAACATTTCCACAGCTTCACAACCACAAAATTTTGTCTCAGGATTTCCACCAAATAGCAATGAAATCAAAAACTGGCAGGATGGACTCAGAGCACTTTTACCAAACATAAACATAAATTTCTCAGATTCTCTGTTATCTCAACAACAAACTTCTTGGCATCATTCAGCACCTTTGACAGAACAGCATTACCCTGACTGGCCTTTTTTTTCACAGCAAGCACAAAGCCCATTCCAAGTACGCCCTCCTCCAGGATTTGAATGTAAATCACCTACAAGCCACCACATGCCAATGCTTGATGATCCAGGTATTTTATGGTCAAAAGCACTTGACACAGGCAATCCTCGAGGAAACAATCTTGCAAGACCAGTTTCTAATGGATATCCAGGAATGCATCCTTTTAGGAGACAAGCAGAACCTCAGAGCACTGCGGCAGTCTCGTCAGCAGAGAAGCTGAAGGAGAGCTCAAGTATCGAATCCTCACATGAGGAAGTTAACTCTGGTACAAGAACAAAAGAATTACTACCAGTCTCGGAGCCTTTAGCAGATGATATAACAATTACAATGACGGAAGGAACTCACGGAGTTAACCCGTCATCAGGATTAACAAATTGTATCAAACAGCGCAAAACAAGAGTGAGTGAGTTATCCATCATCGACGTCAACGACCCTCTTCCAACTCATTGTGCGAATTCGTTGTTGGAGCACAACACTGAAAAGAAAAAACGGGACAGCAGAATACAGGAGACTAACAGACAATACAAACATGGGCAAATCCAAGGAGTAAATAAGAGAGACGAGAGACAGTCTCAACAGAGTAGACATTCAGGTACCAAGACCAGACAAAGTGAGACAACAGGAGGCTCTACCAGGAAACAAACTCATTCTCATCAAGACAGTGATAATTCCCATATGAAGGCAGTTCCTTCTCAGTATTATGATAAAAGAAGAAAAGATTACACAAGTGGATCTGTGGGATAG

Transcript

rna-Spis908_mrna

TGACAAGCGAAGGAAGGGAAATTGGGCAAGAGCGCGAGGGTTTTTCCGCAAGAAATATTTATTGCTTGCTTCATTTCTTCTTGTCTTTGGAGATTTCTGAACTCTCTGGAATCCCAGGGAAACGAAGAACTCGCTGTCCATCGAACACACCGACAGTTTCCGCCGACATTTCTGTTTCCGGTGAAACGTTtcaaaagttgtctatttcgTCCCGTCAAGAAATTAACTACAATACTTTGTACACCGAATAGCTTCTTATTTCTGCAATTAAATTGTCTGACTAGACGGCTTTTTAAGATCATCATGCAAGCTTCCGATGCAGAGTGCCCGTTGTGCATGGAACAGTTGGAAATTGACGACGTCAATTTCTTCCCTTGCACTTGTGGATATCAGATCTGCAGGTTTTGCTGGCATCGTATTAGAACAGATGAGAATGGTTTATGTCCTGCTTGTAGgaagCCCTACAGTGAAGATCCTGCAGTTTATACCCCCCTATCACAAGACGAAATACAGAGAATTCTGAAAGAGAGGAAACAGAAAGATGTACAGAGAAAACAGAAAGTAACTGAGAACAGAAAACATTTAGCAAATGTGAGAGTTGTACAGAAAAATTTGGTATTCGTAGTTGGATTAACTCAAAGATTAGCAGATCCTGAGCTTCTTAAAAGACCAGAGTACTTTAGCAAGTTTgggaaaatacacaaaattgTTGTGAATAACAGTACAAATTATGCAGGACCCCAGGGTCCCAGTGCGAGTGCTTACATTACATATGTGAAAGAAGAGGATGCAATTAAAGCGATAATAGCCGTGTGTAACACTCATCTTGATGGGAGAACACTAAAggCATCTCTGGGGACAACAAAATATTGTAGTTACTTTCTTAGAAACATACCCTGTCCTAAAATGGATTGTATGTATCTTCATGAGTTAGGTGATGGAGCAGGAAGCTTTACAAAGGATGAAATGCAGGCAGGAAAACATCAAGAATATGAACAGCAGTTGATTGCTTTTTATTCGAAGAAAATGGGTCTTAGCAATGATAAGgaTAAAAATGAAGAGTGGCCAGTTGAAGATGGTGGTGAAAACAGAGTATCCCCTCATCTTCCTTCAGGAGGAGCTTGGGCTGGCAAAGATGAGGACGAAGAAGGAGTTACCTGTCAAAATATTTCAGAGAATGAAGATAGTTCAGTTCGAGATAGAAAGGTGGAGGACTGGGAGGAATTGTGTCTCCCATCTGCTACTACAACTACAACAGAACATAAGCCATCCGATACCATAAGACAAGAACAACCAGCAAACCCTCCACAGTCAACGTACAGCAATGCTGGTTGGGGAAATACAGAAAGTGCTGGACGTGCTTTAGAtacCTCTGGTCTGTTCTCTGCTGATCTCTGCAGTGGTCTGGGCCTTTCTAACTTACATCTGAAAGTTGATGGTGAAGATGATTTAGgttttgatCCTTGGAATGAGTGCAGTAAAGGTTTGGCAGATCTTCTtcaagaggaaaacaaaacaacagtgCCTGGACAGACACATAACATTTCCACAGCTTCACAACCACAAAATTTTGTCTCAGGATTTCCACCAAATAGCAATGAAATCAAAAACTGGCAGGATGGACTCAGAGCACTTTTACCAAACATAAACATAAATTTCTCAGattCTCTGTTATCTCAACAACAAACTTCTTGGCATCATTCAGCACCTTTGACAGAACAGCATTACCCTGACTGGCCTTTTTTTTCACAGCAAGCACAAAGCCCATTCCAAGTACGCCCTCCTCCAGGATTTGAATGTAAATCACCTACAAGCCACCACATGCCAATGCTTGATGATCCAGGTATTTTATGGTCAAAAGCACTTGACACAGGCAATCCTCGAGGAAACAATCTTGCAAGACCAGTTTCTAATGGATATCCAGGAATGCATCCTTTTAGGAGACAAGCAGAACCTCAGAGCACTGCGGCAGTCTCGTCAGCAGAGAAGCTGAAGGAGAGCTCAAGTATCGAATCCTCACATGAGGAAGTTAACTCTGGtacaagaacaaaagaattacTACCAGTCTCGGAGCCTTTAGCAGATGATATAACAATTACAATGACGGAAGGAACTCACGGAGTTAACCCGTCATCAGGATTAACAAATTGTATCAAACAGCGCAAAACAAGAGTGAGTGAGTTATCCATCATCGACGTCAACGACCCTCTTCCAACTCATTGTGCGAATTCGTTGTTGGAGCacaacactgaaaagaaaaaacgggACAGCAGAATACAGGAGACTAACAGACAATACAAACATGGGCAAATCCAAGGAGTAAATAAGAGAGACGAGAGACAGTCTCAACAGAGTAGACATTCAGGTACCAAGACCAGACAAAGTGAGACAACAGGAGGCTCTACCAGGAAACAAACTCATTCTCATCAAGACAGTGATAATTCCCATATGAAGGCAGTTCCTTCTCAGTATTatgataaaagaagaaaagattaCACAAGTGGATCTGTGGGATAGAGGAATTGTGTTGGAAAAGAGCAATAAAGTACAAGCTGAAATTGACTTAACACTGAGTGGCTTGTGCAGGGTTTGGACAGAAAAGTCACTGACGCACTGAAGCAAATCAAGGTAATGAGTGCGAGGTATGGGTTTCAAGTCAGCCTTcagaaactgcaaaacaaattgaaacaatgCGATCAACAGATGCCTTTTCGTTAGGTGCAAGTTCACACTATGAATGTTCTGGTGAACCCACGGTGTAAAGGCacaacattaatttttgcaCTCCTATAAGTGATTGGTGAGAAAAATTTCCTAACAATGCCAATATATTGCCAACCAGGCAGGTTACAAGAATCGAGAAAACTATCAGCGTGGAGATTTTTTGACTTAACTGCAATTCTCAGCACTAATCAGTGAAGAAACGTACAATATTCACCAGGAGAAGTTAGTTTTTATATATCTGgagtaaaagttttttttttattttatgctAACTGTCGGCTTACCTTGTTTTAGCTTCTAACCAACCTGTTCACATCTTGCCAAGTATTCTTAAGTTTTAAGAATACTTAAAAAGGAAAGGTTATCGTAGGCAAAGCTTGTTTAACGTTGAATATTccaactgaaaaaaagtttCCATCTCTGTCACGATGATGTACCAGGAAACAGGAAAGCCGAAAACCTGTCTCTTGACAAGGTGATGTGTTTGAATATTAGGATATCTTTTACCATTAACTATTGCTCCTTGCAATTTGTCCTGTCTAACTTCCATCAGCGTTTTAAACAGTGATAGCTGTCTGTGTTGACATGGTTCTTGAGAGAGAAAAGTTACCAACAGACAGACACCTTACAGGTCATTTGCCGTCACATTCCTCCTAATGTCGGTCTGCGAGATCCTATAATTTATATAGCGACAAATCACGTTGGACGAGAAAGGGGTGATAAAACTTCTCAAGCTATCTTCGGAAGAAGTGTGTCTAATAATTCTGTCTTAGAATGCATGCAGTAAATTTCTAACTCTTGGATTTGGCCTCGCTTGCGAGTTTGGCACCGTAAAGAGACGAATCCCAGGTTGGGATTTGGTTCCATGCCCACTCTGTTAGCAGCCATTCAACAAGTAGGAAAAAGACTGTTTGTTAGTCTCCTGTTTAAAGTaaactataaaataataaatgagcCAATTTAC

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003288 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14570 all species →	zf-RING_4	RING/Ubox like zinc-binding domain	Domain	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR039780 all species →	Family	CCR4-NOT transcription complex subunit 4	Interproscan
IPR034261 all species →	Domain	CNOT4, RNA recognition motif	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR039515 all species →	Domain	NOT4, modified RING finger, HC subclass (C4C4-type)	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR003954 all species →	Domain	RNA recognition motif domain, eukaryote	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12603 all species →	CCR4-NOT TRANSCRIPTION COMPLEX RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0030014 all species →	Cellular Component	CCR4-NOT complex	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	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
K10643	CNOT4, NOT4, MOT2; CCR4-NOT transcription complex subunit 4	EC:2.3.2.27	Ubiquitin system	ko04121	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 Stylophora pistillata 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 Stylophora pistillata, 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
SPIST_whole_adult	Whole adults · Adult tissues/organs	13,896	25	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 →