Gene detail

Detailed information of Csp0G456850 in Chrysogorgia sp. JL179-B06

Genomic Location: Contig00837:210276...218113
NR annotation: no NCBI-NR hit recorded
Species Chrysogorgia sp. JL179-B06 · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Csp0G456850

ATGACTTCTATCATCAAGTTAACAGTGTTATCAGGAGGCCAGGATGAATCTCCACTTGCTTACCTTTTACAAGTAGACGAATTTCGCTTCCTGTTAGATTGTGGCTGGGATGAATTTCTTTCACTGGAAACCATTGAGCCGATAAAAAGACATATTAACCAAATTGATGCTGTATTAATCAGTCATCCTGATGTTTATCATCTTGGTGCTTTACCCTACCTCATTGGAAAAGGTGGACTAAGTTCTCCTGTCTATTGTACTATTCCTGTCTACAAAATGGGACAAATGTTCATGTACGACCTTTATCAGTCCCGTCACAATTACGAGGATTTTGACTTGTTCTCCCTTGACGACGTTGATGCAGCATTCGATAAAATAATTCAACTCAAGTATTCCCAGCATGTCAGCTTAAAAGGAAAAGGCCATGGTTTGACAATCACTCCTTATGCTGCTGGTCACATGATTGGTGGTACGATGTGGAAAATTGTTAAAGATGGCGAAGAAGACATTATTTATGCCGTCGATTACAATCATAAAAAAGAAAGGCATTTAAACGGAGCTGTTTTGGAGACCTTAAGCCGACCTTCATTACTTATTGCTGATTCTTTTAATGTTTTGAATGTTCAAGCAAGAAGAAGAGACAGAGATACTCAGTTGATGTCACAAATATTGAAAACAACAAGAAGAGGAGGCAATGTGCTACTTGCTGTGGATACTGCTGGAAGAGTACTAGAGCTGTCTCAGTTGCTGGATCAACTATGGCGCAATCCAGATTCCGGATTGTTTGCGTATTCCTTGGCATTGTTGAATAATGTCAGTTATAATGTGATTGAATTTGCCAAGTCTCTAGTAGAGTGGATGAGTGACAAGGTAATGAAGACTTTTGAAGTGGGCCGGGCTAATCCTTACCAATTCAAGTATTGTAAGCTCTGTCACAACTTAGCAGAGTTGGCAGAGGTTCCATCACCAAAAGTTGTGTTGGCCAGTATGCAGGATCTAACCTCTGGTTTTGCGAAAGATCTTTTTGTGGAGTGGGCAGAAGATGAAAAAAATAGTGTAATTTTTTCAACAAGAACTTCTCCTGGTTCATTGGCAAGAAAACTTATTGACAATCCCACTACTACTAAAGTAGAAGTTGAGATAAAAACTAGAATAAAACTCGAAGGGGAAGAATTAGAAAAACATTTGGAAATGCAAAGGGAGGAAGAAAAGGATAAAAAGATGACAGAAGCAAGTGATAAAAGTAAAGAAACTGTTGAAGCAAGCGACAGTGACAGTGAAGATGAGGGTATAGACTTAATGTTTGGAGGGAGAAGTCGACATGATCTTATGATGACTGATGAAAAGAGAGGTAACAAAAGCAGTTTCTTCAAGCAGGCCAAGTCTTACCCCATGTTTCCTTGTAAAGAAGAGAAGGTCAAATGGGACGAGTATGGTGAAATTATAAGGATGGAAGATTTTTTGATACCTGACACTGCTATTGCAGAAGAAGAAAAGAAAAAAGTTGAGCAAGACTCTGGGACTTCAGACACTGAGGCAGTTATGGGGCCAGATGAACCTGTTAATGTGCCGACTAAATGCATAGTAGAGAAACGGACACTTAATATCAAATGCTCTTTGGTCTACATCGACTTTGAAGGTCGGTCAGATGGCGAATCTATAAAAAGAATCATATCCATTGTTAAACCAAGGCAATTGGTTTTGATCCATGGTAATTCTGATGCAACTACAAGTTTAGCTGAGTACTGTCGAAAAAATACTGATATGGAAGTCAAGAAAGTGTATACTCCTGCTACAGGAGAAACTGTCGATGCAACAAGGGAAAGCCATATTTATCAGATAAAGCTGAGGGACTCCTTGGTCAGTGCTCTCCAATTTTCTCAGACACGTGATGCTGAGATTGCCTGGGTCGATGGACAACTTGTGAAAGAGAATATAAAATCTCTGACTCAAACATCTAATGATGTTGAGAAAATGGATGTTGATAGGGTAGATACTTTTGATTCCGTACCAGTGTTGGAACAACTAGCTTTGACTGAGATTCCTGGTCATGATCAAGTGTTTATCAATGACCCAAGACTGTCAGACTTTAAACAAATTCTCCAAAAGAATGGGTTACAGAATGAAGCTGGCCGTATTGGTATAGATGGAGCTGTCTGTGATGAATACTACAAGATAAGGGAGTTGCTATATGAACAGTTTGCTATTTGCTAG

Transcript

Csp0G456850

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004930 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10996 all species →	Beta-Casp	Beta-Casp domain	Domain	Interproscan
PF07521 all species →	RMMBL	Zn-dependent metallo-hydrolase RNA specificity domain	Motif	Interproscan
PF13299 all species →	CPSF100_C	Cleavage and polyadenylation factor 2 C-terminal	Family	Interproscan
PF16661 all species →	Lactamase_B_6	Metallo-beta-lactamase superfamily domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR022712 all species →	Domain	Beta-Casp domain	Interproscan
IPR036866 all species →	Homologous_superfamily	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Interproscan
IPR011108 all species →	Domain	Zn-dependent metallo-hydrolase, RNA specificity domain	Interproscan
IPR035639 all species →	Domain	CPSF2, metallo-hydrolase domain	Interproscan
IPR025069 all species →	Domain	Cleavage and polyadenylation specificity factor 2, C-terminal	Interproscan
IPR001279 all species →	Domain	Metallo-beta-lactamase	Interproscan
IPR027075 all species →	Family	Cleavage and polyadenylation specificity factor subunit 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45922 all species →	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005847 all species →	Cellular Component	mRNA cleavage and polyadenylation specificity factor complex	Interproscan
GO:0006378 all species →	Biological Process	obsolete mRNA polyadenylation	Interproscan
GO:0006398 all species →	Biological Process	mRNA 3'-end processing by stem-loop binding and cleavage	Interproscan
GO:0098789 all species →	Biological Process	obsolete pre-mRNA cleavage required for polyadenylation	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
K14402	CPSF2, CFT2; cleavage and polyadenylation specificity factor subunit 2	-	Messenger RNA biogenesis	ko03019	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 Chrysogorgia sp. JL179-B06 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 Chrysogorgia sp. JL179-B06, 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 →