Gene detail

Detailed information of g68.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: MCH1521138.1, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase [SAR324 cluster bacterium]
Species Calvadosia cruxmelitensis · all data for this species · gene families

Sequence

Sequence data are not available for Calvadosia cruxmelitensis.
Nucleotide and protein sequences are provided for the species whose genome annotation is complete (see annotated genomes); for this species only the assembly is archived. The functional annotation below is likewise unavailable.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q2RFM0	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase OS=Moorella thermoacetica (strain ATCC 39073 / JCM 9320) OX=264732 GN=ispD PE=3 SV=1
A8F958	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase OS=Bacillus pumilus (strain SAFR-032) OX=315750 GN=ispD PE=3 SV=1
A5D5L4	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase OS=Pelotomaculum thermopropionicum (strain DSM 13744 / JCM 10971 / SI) OX=370438 GN=ispD PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000001 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000006 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000047 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000126 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000781 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000852 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001484 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001674 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003785 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0011522 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0019357 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0030287 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0037179 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0062099 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF13843 all species →	DDE_Tnp_1_7	Transposase IS4	Domain	Interproscan
PF00233 all species →	PDEase_I	3'5'-cyclic nucleotide phosphodiesterase	Domain	Interproscan
PF01128 all species →	IspD	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	Family	Interproscan
PF00083 all species →	Sugar_tr	Sugar (and other) transporter	Family	Interproscan
PF07690 all species →	MFS_1	Major Facilitator Superfamily	Family	Interproscan
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan
PF00155 all species →	Aminotran_1_2	Aminotransferase class I and II	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR050886 all species →	Family	RNA-binding_regulatory_proteins	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR029526 all species →	Domain	PiggyBac transposable element-derived protein	Interproscan
IPR002073 all species →	Domain	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Interproscan
IPR036971 all species →	Homologous_superfamily	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Interproscan
IPR018294 all species →	Conserved_site	4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site	Interproscan
IPR029044 all species →	Homologous_superfamily	Nucleotide-diphospho-sugar transferases	Interproscan
IPR050088 all species →	Family	IspD/TarI cytidylyltransferase	Interproscan
IPR034683 all species →	Family	Cytidylyltransferase IspD/TarI	Interproscan
IPR020846 all species →	Domain	Major facilitator superfamily domain	Interproscan
IPR005829 all species →	Conserved_site	Sugar transporter, conserved site	Interproscan
IPR036259 all species →	Homologous_superfamily	MFS transporter superfamily	Interproscan
IPR005828 all species →	Family	Major facilitator, sugar transporter-like	Interproscan
IPR011701 all species →	Family	Major facilitator superfamily	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan
IPR001917 all species →	Binding_site	Aminotransferase, class-II, pyridoxal-phosphate binding site	Interproscan
IPR004839 all species →	Domain	Aminotransferase, class I/classII	Interproscan
IPR015422 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, small domain	Interproscan
IPR015421 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase, major domain	Interproscan
IPR015424 all species →	Homologous_superfamily	Pyridoxal phosphate-dependent transferase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48024 all species →	GEO13361P1-RELATED	Interproscan
PTHR46599 all species →	PIGGYBAC TRANSPOSABLE ELEMENT-DERIVED PROTEIN 4	Interproscan
PTHR46704 all species →	CXC DOMAIN-CONTAINING PROTEIN-RELATED	Interproscan
PTHR11347 all species →	CYCLIC NUCLEOTIDE PHOSPHODIESTERASE	Interproscan
PTHR32125 all species →	2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC	Interproscan
PTHR23511 all species →	SYNAPTIC VESICLE GLYCOPROTEIN 2	Interproscan
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR42885 all species →	HISTIDINOL-PHOSPHATE AMINOTRANSFERASE-RELATED	Interproscan
PTHR47018 all species →	CXC DOMAIN-CONTAINING PROTEIN-RELATED	Interproscan
PTHR45823 all species →	T-SNARE COILED-COIL HOMOLOGY DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004114 all species →	Molecular Function	3',5'-cyclic-nucleotide phosphodiesterase activity	Interproscan
GO:0007165 all species →	Biological Process	signal transduction	Interproscan
GO:0004115 all species →	Molecular Function	3',5'-cyclic-AMP phosphodiesterase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0048471 all species →	Cellular Component	perinuclear region of cytoplasm	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0008299 all species →	Biological Process	isoprenoid biosynthetic process	Interproscan
GO:0050518 all species →	Molecular Function	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	Interproscan
GO:0070567 all species →	Molecular Function	cytidylyltransferase activity	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0016021 all species →	Cellular Component	membrane	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0016740 all species →	Molecular Function	transferase activity	Interproscan
GO:0009058 all species →	Biological Process	biosynthetic process	Interproscan
GO:0030170 all species →	Molecular Function	pyridoxal phosphate 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
K00817	hisC; histidinol-phosphate aminotransferase	EC:2.6.1.9	Amino acid related enzymes	ko01007	deepkoala
K00991	ispD; 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	EC:2.7.7.60	Terpenoid backbone biosynthesis	ko00900	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 Calvadosia cruxmelitensis 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 Calvadosia cruxmelitensis, 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.	sequence table not available	–
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.	sequence table not available	–
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 →