Gene detail

Detailed information of g20.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: WP_044431616.1, tRNA pseudouridine(38-40) synthase TruA [Skermanella aerolata]
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
Q0ASJ7	tRNA pseudouridine synthase A OS=Maricaulis maris (strain MCS10) OX=394221 GN=truA PE=3 SV=1
Q2WAT0	tRNA pseudouridine synthase A OS=Paramagnetospirillum magneticum (strain ATCC 700264 / AMB-1) OX=342108 GN=truA PE=3 SV=1
Q07TX2	tRNA pseudouridine synthase A OS=Rhodopseudomonas palustris (strain BisA53) OX=316055 GN=truA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000034 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000045 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000073 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000418 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000853 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000990 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001991 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002244 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002277 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004831 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006748 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0018801 (this species only) · gene tree & orthology
Transcription factor family	ZBTB · all TF in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|BTB · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16686 all species →	POT1PC	ssDNA-binding domain of telomere protection protein	Domain	Interproscan
PF01416 all species →	PseudoU_synth_1	tRNA pseudouridine synthase	Domain	Interproscan
PF08763 all species →	Ca_chan_IQ	Voltage gated calcium channel IQ domain	Domain	Interproscan
PF16905 all species →	GPHH	Voltage-dependent L-type calcium channel, IQ-associated	Family	Interproscan
PF10188 all species →	Oscp1	Organic solute transport protein 1	Family	Interproscan
PF15734 all species →	MIIP	Migration and invasion-inhibitory	Family	Interproscan
PF16177 all species →	ACAS_N	Acetyl-coenzyme A synthetase N-terminus	Family	Interproscan
PF00852 all species →	Glyco_transf_10	Glycosyltransferase family 10 (fucosyltransferase) C-term	Family	Interproscan
PF17039 all species →	Glyco_tran_10_N	Fucosyltransferase, N-terminal	Domain	Interproscan
PF14291 all species →	DUF4371	Domain of unknown function (DUF4371)	Family	Interproscan
PF05699 all species →	Dimer_Tnp_hAT	hAT family C-terminal dimerisation region	Domain	Interproscan
PF01344 all species →	Kelch_1	Kelch motif	Repeat	Interproscan
PF07707 all species →	BACK	BTB And C-terminal Kelch	Domain	Interproscan
PF00651 all species →	BTB	BTB/POZ domain	Domain	Interproscan
PF00069 all species →	Pkinase	Protein kinase domain	Domain	Interproscan
PF00385 all species →	Chromo	Chromo (CHRromatin Organisation MOdifier) domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR028389 all species →	Family	Protection of telomeres protein 1	Interproscan
IPR032042 all species →	Domain	Protection of telomeres protein 1, ssDNA-binding domain	Interproscan
IPR001406 all species →	Family	Pseudouridine synthase I, TruA	Interproscan
IPR020097 all species →	Domain	Pseudouridine synthase I, TruA, alpha/beta domain	Interproscan
IPR020103 all species →	Homologous_superfamily	Pseudouridine synthase, catalytic domain superfamily	Interproscan
IPR020094 all species →	Homologous_superfamily	Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal	Interproscan
IPR020095 all species →	Homologous_superfamily	Pseudouridine synthase I, TruA, C-terminal	Interproscan
IPR014873 all species →	Domain	Voltage-dependent calcium channel, alpha-1 subunit, IQ domain	Interproscan
IPR011992 all species →	Homologous_superfamily	EF-hand domain pair	Interproscan
IPR031649 all species →	Domain	Voltage-dependent L-type calcium channel, IQ-associated domain	Interproscan
IPR050599 all species →	Family	Voltage-dependent calcium channel alpha-1 subunit	Interproscan
IPR019332 all species →	Family	Organic solute carrier protein 1	Interproscan
IPR031466 all species →	Family	Migration and invasion-inhibitory protein	Interproscan
IPR032387 all species →	Domain	Acetyl-coenzyme A synthetase, N-terminal domain	Interproscan
IPR042099 all species →	Homologous_superfamily	ANL, N-terminal domain	Interproscan
IPR001503 all species →	Family	Glycosyl transferase family 10	Interproscan
IPR038577 all species →	Homologous_superfamily	GT10-like, C-terminal domain superfamily	Interproscan
IPR031481 all species →	Domain	Fucosyltransferase, N-terminal	Interproscan
IPR025398 all species →	Domain	Domain of unknown function DUF4371	Interproscan
IPR008906 all species →	Domain	HAT, C-terminal dimerisation domain	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR052958 all species →	Family	Interferon-induced PKR regulator	Interproscan
IPR006652 all species →	Repeat	Kelch repeat type 1	Interproscan
IPR015915 all species →	Homologous_superfamily	Kelch-type beta propeller	Interproscan
IPR011333 all species →	Homologous_superfamily	SKP1/BTB/POZ domain superfamily	Interproscan
IPR011705 all species →	Domain	BTB/Kelch-associated	Interproscan
IPR000210 all species →	Domain	BTB/POZ domain	Interproscan
IPR017096 all species →	Family	BTB-kelch protein	Interproscan
IPR000719 all species →	Domain	Protein kinase domain	Interproscan
IPR008271 all species →	Active_site	Serine/threonine-protein kinase, active site	Interproscan
IPR011009 all species →	Homologous_superfamily	Protein kinase-like domain superfamily	Interproscan
IPR036770 all species →	Homologous_superfamily	Ankyrin repeat-containing domain superfamily	Interproscan
IPR000953 all species →	Domain	Chromo/chromo shadow domain	Interproscan
IPR023779 all species →	Conserved_site	Chromo domain, conserved site	Interproscan
IPR023780 all species →	Domain	Chromo domain	Interproscan
IPR016197 all species →	Homologous_superfamily	Chromo-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14513 all species →	PROTECTION OF TELOMERES 1	Interproscan
PTHR21301 all species →	REVERSE TRANSCRIPTASE	Interproscan
PTHR11142 all species →	PSEUDOURIDYLATE SYNTHASE	Interproscan
PTHR45628 all species →	VOLTAGE-DEPENDENT CALCIUM CHANNEL TYPE A SUBUNIT ALPHA-1	Interproscan
PTHR21439 all species →	OXIDORED-NITRO DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR34831 all species →	MIGRATION AND INVASION-INHIBITORY PROTEIN	Interproscan
PTHR11929 all species →	ALPHA- 1,3 -FUCOSYLTRANSFERASE	Interproscan
PTHR46289 all species →	52 KDA REPRESSOR OF THE INHIBITOR OF THE PROTEIN KINASE-LIKE PROTEIN-RELATED	Interproscan
PTHR24412 all species →	KELCH PROTEIN	Interproscan
PTHR31424 all species →	PROTEIN CBG23806	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000723 all species →	Biological Process	telomere maintenance	Interproscan
GO:0000783 all species →	Cellular Component	nuclear telomere cap complex	Interproscan
GO:0010521 all species →	Molecular Function	telomerase inhibitor activity	Interproscan
GO:0016233 all species →	Biological Process	telomere capping	Interproscan
GO:0032210 all species →	Biological Process	regulation of telomere maintenance via telomerase	Interproscan
GO:0043047 all species →	Molecular Function	single-stranded telomeric DNA binding	Interproscan
GO:0051974 all species →	Biological Process	obsolete negative regulation of telomerase activity	Interproscan
GO:0098505 all species →	Molecular Function	G-rich strand telomeric DNA binding	Interproscan
GO:0001522 all species →	Biological Process	pseudouridine synthesis	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0009451 all species →	Biological Process	RNA modification	Interproscan
GO:0009982 all species →	Molecular Function	pseudouridine synthase activity	Interproscan
GO:0031119 all species →	Biological Process	tRNA pseudouridine synthesis	Interproscan
GO:0005891 all species →	Cellular Component	voltage-gated calcium channel complex	Interproscan
GO:0008331 all species →	Molecular Function	high voltage-gated calcium channel activity	Interproscan
GO:0098703 all species →	Biological Process	calcium ion import across plasma membrane	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006810 all species →	Biological Process	transport	Interproscan
GO:0010972 all species →	Biological Process	negative regulation of G2/M transition of mitotic cell cycle	Interproscan
GO:0030336 all species →	Biological Process	negative regulation of cell migration	Interproscan
GO:0006486 all species →	Biological Process	protein glycosylation	Interproscan
GO:0008417 all species →	Molecular Function	fucosyltransferase activity	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0036065 all species →	Biological Process	fucosylation	Interproscan
GO:0046920 all species →	Molecular Function	alpha-(1->3)-fucosyltransferase activity	Interproscan
GO:0046983 all species →	Molecular Function	protein dimerization activity	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0004672 all species →	Molecular Function	protein kinase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006468 all species →	Biological Process	protein phosphorylation	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
K06173	truA, PUS1; tRNA pseudouridine38-40 synthase	EC:5.4.99.12	Transfer RNA biogenesis	ko03016	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 →