Gene detail

Detailed information of Csp0G477360 in Chrysogorgia sp. JL179-B06

Genomic Location: Contig00855:250535...310671
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

Csp0G477360

ATGTTAGTGCTGACACTCTTGCTAAATGGTGGGTTGAACCAAATGATATTGCTAAGTTACAGCTGCATGAACAATGAAAGTCCAAAAGGCAGGAAGAAAATGACCCAAACCAATATTTTAGATTTGTTTTCCAGAAAGTCTAATAAAAGAAAGAAGAGCAATGAGAAAGAGAAATGTGAAAACAACGATGCAAACGAAAACGAAATGTTACTAGCGACGACGAAGTCCGAATTAACTCTCGTCTCAGAAATTGAGGGCGAAAAATCTAGTTGTTTTAATAAAAACTATCTTATGTTCATCCCCACAAAGTGTTCCGAATGCGGTCAGTTATTGGACAGCCCTAATCTTCATCTGTTTAGTGGTGATGTCGATGATGCAGTTGAAGAGTTTGTGATGTTGGTTGATCCCAAGCTTTCCCTGTTTACCGGAGATGAAACTACATATGGAAGTTATGAAGTGGATCGGCCACAACATAAGATTACGCAGTTCAGTGTCTATGACAAGTCTACGCATCTGTGTCCATTTGATAATGGTCTGATTGAGAAAAACAAGGAATTGTTTATCTCTGGATATGTGAAACCAATATATGATGAAAACACAAGCTCTGATGGTGGCGTACCAGCCAAAGCTATTGGTCCGATTAACGAATGGTGGACTACAGGTTTTGATGGCGGGGAAAATGTTGTCATAGGAATAACTACCGCATTTGGTGAATATGTATTAATGGCTCCCTCAGAGGAATATCGTCCAGTTATGGATGCTATGAAAGAGAAAACCTTCCTTAGTAAGATCGTAATAGAATTTCTTTTGGAATATCGTGATTCTAGATATGAAGATTTGCTCAATAAAATTGAGACGTCAGTTCCGCCGGATGGAGCTACAAGTTTGACCGAAGATTCTCTTCTGAAGCATGCGCAGTTCCTCGTCGAACAGGTTGAGAATTTCGACTCTGCCGGTGAAGAAGATGAACTACCATTACTAGTCACACCATGTATGAGAGATCTGATTAAACTGGCTGGAGTGGTTCTTGGAAAAAGGAGAAATCCTCGTGGAATAAGAGTAAAACCAGAGAAAAAGAAGAAAGATGAACCTACGAAGGCTACTACAACACCGTTGGTTCGCTATGTCTTCGACATTTTTTTCCAAAACCAAATAGACGGCAAACAAGACAGGACAGTAAAACGCAGCCGTTGTGGCGTTTGTGAAACATGTCAGCAACCGGACTGTGGGCAGTGCAGAGCCTGTCGGGATATGGTAAAGTTTGGGGGAACTGGACGTGCAAAACAATGTTGTATCAATCGAAGGTGTCCAAACATGATTGTCCGACAAGCGGATGAAAACGACGTTGACGCACAAGACCAAGAATTGGAAAAGGAAACGAAAGATAAGAAAAAGGGGAAAGATGGAAAGCGAAAATGCGCGAAACTACAAAATGTCATCAAGACAAAACTGAAATGGATTGGACAACCTGTGGAAATTCAAGGCAAAAGGACCTACTATCTTAGCGTTGAAGTCAATGATGAACAGGTTACCATTGGAGAGTATGTCAAACTTTGTCCTAGCAATCCAACGGTGCCATTGTACATTTGTAAAGTTATTTCTATGTGGGAAAATGTTCGTGGAGAGAAAATGTTCCACGGACATTGGATGAGCCGTAGTTGTGAAACTATTCTTGGTAATACTGGTGATCCCATGGAACTGTTTCTCACTGACCAATGCGAGGACAATCCTTTGGGATCTGTTATGGCCAAATGTTATGTTACGTATAAAGCCCCTGGTAATGATTGGTTTAGTAAGGGTGGTGAAGAAGTTAGCGATGTTGAAAGAGGTGAAGATGATGGAAATCATTTCTTCTTTCAAATGTGGTACGACGAGGAACATGCTCGATTCGAACAACAGCTAAAAGATTATCAGAAAAATGAAGAAGATAGTGGTTGCATTAGCTGCTATAGACAAGAGAAAGATCGACAGCTTGAAACACCAACTCTTGGGGAAGCTTTGGATTCTGAAGATAGCAAGTCAAAAAGCAGCACTTATAGATCATTTTCCCTCGACGGTGTTCAATATCGAATTGGAGATGCAGTTTACCTTATTCCAGAGGCGTTTGCCTTCAAGGTTAAACCAGCTGAGACGAAAAAGACAGCTAAAAAAGGAAACGATAAGAGTGATGAGGATATATATCCAGAGTACTATCGTAAATCATCTGACTACATCAAAGGAAGCAACACCGCTGTCTCACAGCCGTTCAGAATTGGTGAAATTCTTTCCATTTCGCGAAAAACGACTTTCAGTAGCCTCAAAGATGACACACCCGAGATAAGATTGAAAGTACGAAAGTTTTACAGGCCAGAGAATACTCATAAAGGCCCGAAAGCAGGTTACCAGACAGACTTAAACCTAGTTTATTGGAGTTCTGAAGAGGTTGGTGTTGATATAAAGATGTTGATGGGCAAATGTACTGTAGTGTATGTTGGTGACTTGGATATTGACACAGGAGAATATATCAACCAAGGACCTGATAGATTCTACTTTATTGAGGCGTACAATTCCGAGACTTTGGAAATTGAAGACGTTCCTGATGATGCTAGAAAGACGTCCGCCAAAGGAAAGGGCAAAGGAAAGGGGAAAGGGAAAGGGAAAGCTACAGTTGATCCAGTTCCTAAAACTATCAATGGAGAAAATAAAACAGAAGAGATCAAGAAGCTGGGAACCCTTGATGTTTTCGCTGGATGTGGAGGTCTGTCAGAAGGTCTCCATCAAGCAGGCATAGCAGATACACGTTGGGCAATTGAGATTGATGAACCAGCTGCTCAATCTTTCCGCGCTAACAACTCACGGACCACAGTGTTTACAGATGACTGCAATAAGTTACTAAAACTAGTTATGGAGGGCGAGAAAGAGAATACACGAGGGCAGTCGCTGCCGAAACAAGGAGATGTTGAATTGCTTTGTGGTGGACCACCTTGTCAAGGTTTTAGTGGAATGAATCGTTTCAGTTCCAGAGAGTATTCTGGTTTTAAGAATTCCTTAGTAGCGACCTATCTCAGCTACTGTGACTACTATCGCCCGAAGTTCTTCCTGTTGGAAAATGTGCGCAACTTCGTGTCTTTTAAAAAAAGCATGGTCTTGAAACTGACGTTGAGATGCCTACTGAAGATGGGGTACCAGTGTACCTTTGGCGTTCTTCAAGCAGGTAGTTACGGTGTCCCTCAAACTCGTCGTCGTGCTATTATTTTGGCTGCAGCTCCTGGACAAGTTCTTCCGATGTTTCCTGAACCAACTCATTGCTTTGCTCGTCGAGCTTGTCAACTCACTGTTTTGGTCGATGACACAAAGTATATTTCGAATATCGAACGTGTTGATTCAGCTCCGTATAGAACTGTCACCGTGCGAGATGCCATGTCAGATCTGCCTGAGATACGGAATGGTGCAAGTGCCATTGAAATATCGTATGGTGGAGAAGCTCAATCTCATTTTCAGAGAAAGATCCGTGGTAAAGACGACAAGGTGGCGCTTCGCGATCACGTATGTAAAGAAATGGCCCCTCTGGTTGTGGCAAGGATTCAACGTATTCCCCAGGAGCCTGGCTCAGATTGGAGAGATTTACCCAATATCTCCGTGAGATTAACAGATGGAAAATATACTGAAAAACTACGATACACTCACGTGGACAAGAAGAACGCAAGTAGCTCGACTGGTCAACGAAGAGGTGTGTGTAGTTGTGCAGAGGGAGAACCATGTGACCCAGCTGATCGACAATATAATACCCTTGTACCGTGGTGTCTACCTCACACTGGCAATAGACACAACCATTGGGCTGGACTGTATGGAAGACTAGAGTGGGATGGCTATTTTAGTACAACGATTACTAACCCAGAGCCAATGGGAAAACAGGGTCGTGTCCTTCATCCGTCACAGCATCGGGTTGTTAGTGTGCGTGAATGTGCTCGTTCTCAGGGCTTCCCAGATACCTACCGCTTTATAGGAGAAGTATTGGATAAACATAGACAAATTGGGAATGCTGTTCCACCTCCCATGGCTAAAGCTATCGGTCTCGAAATGAAAAAATGTTTATTAAAGCTGCAAGAACAGTAA

Transcript

Csp0G477360

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003136 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01426 all species →	BAH	BAH domain	Domain	Interproscan
PF02008 all species →	zf-CXXC	CXXC zinc finger domain	Domain	Interproscan
PF12047 all species →	DNMT1-RFD	Cytosine specific DNA methyltransferase replication foci domain	Domain	Interproscan
PF00145 all species →	DNA_methylase	C-5 cytosine-specific DNA methylase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001525 all species →	Family	C-5 cytosine methyltransferase	Interproscan
IPR031303 all species →	Conserved_site	DNA methylase, C-5 cytosine-specific, conserved site	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR043151 all species →	Homologous_superfamily	Bromo adjacent homology (BAH) domain superfamily	Interproscan
IPR001025 all species →	Domain	Bromo adjacent homology (BAH) domain	Interproscan
IPR002857 all species →	Domain	Zinc finger, CXXC-type	Interproscan
IPR018117 all species →	Active_site	DNA methylase, C-5 cytosine-specific, active site	Interproscan
IPR050390 all species →	Family	DNA Cytosine-5 Methyltransferase	Interproscan
IPR022702 all species →	Domain	DNA (cytosine-5)-methyltransferase 1, replication foci domain	Interproscan
IPR017198 all species →	Family	DNA (cytosine-5)-methyltransferase 1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10629 all species →	CYTOSINE-SPECIFIC METHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003886 all species →	Molecular Function	DNA (cytosine-5-)-methyltransferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0010216 all species →	Biological Process	obsolete negative regulation of gene expression via chromosomal DNA cytosine methylation	Interproscan
GO:0010424 all species →	Biological Process	obsolete DNA methylation on cytosine within a CG sequence	Interproscan
GO:0006346 all species →	Biological Process	DNA methylation-dependent constitutive heterochromatin formation	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
K00558	DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1	EC:2.1.1.37	Prokaryotic defense system	ko02048	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 →