Gene detail

Detailed information of Csp0G315260 in Chrysogorgia sp. JL179-B06

Genomic Location: Contig00600:1657609...1670192
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

Csp0G315260

ATGCACGCAGTCTCCAAGTTCTTCCCCAATAACTGTATCGGGAATGCCAGAAAATGCTTGTACTTCCCTGTATTTCACAACTGTATTCGTTGCTCCAGCCTCGATACTCAGACCGGAGTCCCATACAAAACATTGCAGAGTGATGACACCAAGTTGCCTGATGCAGTGCCACACGAAGCTGATGTCGTGGTAATTGGTGGTGGATCTTTAGGCTCGAGTACACTGTACCATCTTACAAAGCTTGGCATACATAATGCTGTATTGCTAGAGAAAAGTCAGCTAACTGCTGGTACAACTTGGCATAGTGCTGGTCTTGCCTGGAGACTGAGACCAAATGATGTTGATATTGAGTTGCTGAACCACACAAGAGATTTGGCTTGTGAGATTTTGGAGAAAGAAACAGAACTGTCGACTGGATGGATTGGGAATGGTGGACTTTTTATCGCTGCAAATAAAGAGAGATTGGACGAATACAAACGGCTCATGACTCTTGGTAAAATTTTTGGCATCAACTCTCATGTGTTGTCACCAAAAGAGACTAAGGAATTATACCCGTTGATGAATGTTGATGATTTATATGGCACACTGTACAGCCCTGGAGATGGTACTATTGATCCAGCTGGATGGGCAACCACCTTAACCAGAGCTGCAAAAAATAACGGAGCACAGGTTTATGAGAATTGTTCTGTTACTGGAATAACCACTGAAGTTGATGACTTTGGAGTGAAGCGAGTAACTGGTGTGCAGACTCCTGTTGGTCACATCAAAACCAAAGCTGTTGTAAATTGTGCTGGGGTATGGGCTCCATATATTGGCGAAATGGTGGGCGTTGCTGTACCTCTTGTTGCCATGCACCATGCCTACATTGTCACCGAGAAGATTGAAGGCATTGAGAAAATGCCTAATGTCCGAGACCATGATGCATCTGTGTACCTGAAGTTGCAAGGCGATGGCTTATCTGTTGGTGGATATGAAAATAATCCTATATTTTGGGACAAGGTTAGCAACGACTTTGCATTTGGACTTTTCGACCTGGACTGGGATGTTTTTAGCACTCACATTGAAGGGGCAGTAAATAGAGCTCCTATTATTGGAGAAACAGGTGTAAAGTCCACTGTTTGTGGTCCAGAGTCATTTACTGCTGATCATAAACCATTGATGGGTGAGGCACCTGAGGTCCGTGGCTTTTATCTTGGTTGTGGTTTTAATTCTTCTGGAATCATGTTAGCTGGAGGGTGTGGTCGAGAGTTAGCACAGTGGATAACTCGTGGACACCCCACCCTTGATATGTATGGTTATGATATAAGACGTTTCCATACTTCACTTACTTCCAACATTAATTGGTCAAGAGAGAGAAGCCATGAGTCTTATGCTAAGAATTATTCCATTGTTTATCCTCACGATGAGCCCTTAGCAAGCCGTAACATGAGATGTGATCCGTTTCACCAAGTATTACTGGATGCCGGTTGCGTTTACCAAGAACGTTTAGGATGGGAAAGACCAGGGTGGTTTGCCATTGACTCCAAGCCAAAGATCAATGATTATGATTATTATGGAGCATATGAAAATGAAAGAAAAGTGTCTAAATATGAAGAACTGCTTTGCAAAGAGTACACATTTGAATTTCCTGAACATCACAATGTCATTGCAAAAGAATGTGAAACATGCAGGAGTAATGTAGCTGCGTTTAACATGTCATATTTTGGAAAGTTTTACATGACTGGGCCAGATGCTCAAAAAGCCGTAGATTGGATATTTACAAATAATATGCAAAAACTTCCAGGGTCAACAACTTACACCTGTATGTTAAACAAAGATGGAGGGGTCCAAGCCGATGTGACTGTGTCTGTTTTGGAGGAAAATGGTGCACCTAGTGTTCTGTCACCAAAGGCTGAAGGAAGGCGTTTTTATGTGGCTGCTGGTGGAGGTATTGCTCAACATGCCTGGTGTCACATTAAAAATATTCTAGAAGATAAGAGATTTGATTGTCAGTTGATTGATAAATCAGAAGAGATGGGCATGCTGAGCATCCAAGGACCTAAAAGCCGTGAACTGTTGCAGTCCCTTATAGACGTCGACCTTAGCAACGAAACCTTCCCATTTTCAACTCACAAGATTGTCCAGATTGCAGGACATGATGTGCGCATTCTCCGGCTAACATTTGTTGGTGAACTTGGATATGAACTGCATATTCCCATAGCATCTTGTATACCAGTGTACAGCGTCGTCATGGCAGAAGGAGCCAAATATGGCATCATTAATTCTGGCTACCGAGCAATCGACTCCCTCAGTGTCGAGAAAGGATTCAAGCATTGGCACATGGATATCAGGCATGACGACACGCCTTTGGAAGGTGGGCTGGCTTTTACCTGCAAGTTAAAGCTCGATACCCCATTTCTTGGAAGAGAAGCTCTTGAGAAACAGAAGGCTGAAGGGCTGAAGAAAAGATTAATATGTCTCACTTTAGATCAGCACAAAGCTCTTCATGGTCTTGAAGGCATCTACCGTGATGGCCATGCAGTAGGATATCTTCGCCGTGCCGATTTCGGCCACACTGTGAACAAAACCGTCTGTTATGGTTACATCAAACATCATGAAAATGATGTCATCACCACAGAGTACCTAAAGTCTGGCACATACACCATCGATGCCATGGGTGATATCTACCCTGCTACATTGCATATGAAACCAGTATTTGATCCAAAAAACAACCGAGTCAAAGGGGTTTATGAAATTAATAGTAAAAATACCAACAAATTCACAGATGAACTTGAAACCCATACCAGTATCATGTAA

Transcript

Csp0G315260

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001332 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01571 all species →	GCV_T	Aminomethyltransferase folate-binding domain	Domain	Interproscan
PF16350 all species →	FAO_M	FAD dependent oxidoreductase central domain	Family	Interproscan
PF01266 all species →	DAO	FAD dependent oxidoreductase	Domain	Interproscan
PF08669 all species →	GCV_T_C	Glycine cleavage T-protein C-terminal barrel domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006222 all species →	Domain	Aminomethyltransferase, folate-binding domain	Interproscan
IPR036188 all species →	Homologous_superfamily	FAD/NAD(P)-binding domain superfamily	Interproscan
IPR027266 all species →	Homologous_superfamily	GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1	Interproscan
IPR032503 all species →	Domain	FAD dependent oxidoreductase, central domain	Interproscan
IPR006076 all species →	Domain	FAD dependent oxidoreductase	Interproscan
IPR013977 all species →	Domain	Glycine cleavage T-protein, C-terminal barrel domain	Interproscan
IPR029043 all species →	Homologous_superfamily	Glycine cleavage T-protein/YgfZ, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13847 all species →	SARCOSINE DEHYDROGENASE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0005759 all species →	Cellular Component	mitochondrial matrix	Interproscan
GO:0008480 all species →	Molecular Function	sarcosine dehydrogenase activity	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:1901053 all species →	Biological Process	sarcosine catabolic process	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
K00314	SARDH; sarcosine dehydrogenase	EC:1.5.8.3	Glycine, serine and threonine metabolism	ko00260	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 →