Gene detail

Detailed information of g650.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: GFR62201.1, endonuclease-reverse transcriptase [Elysia marginata]
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
Q2G5P7	Probable transaldolase OS=Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199) OX=279238 GN=tal PE=3 SV=1
Q2N908	Probable transaldolase OS=Erythrobacter litoralis (strain HTCC2594) OX=314225 GN=tal PE=3 SV=1
A5V2S4	Probable transaldolase OS=Rhizorhabdus wittichii (strain DSM 6014 / CCUG 31198 / JCM 15750 / NBRC 105917 / EY 4224 / RW1) OX=392499 GN=tal 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)	OG0000009 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000549 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006695 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006783 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0014277 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0014997 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0019869 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0020716 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0025735 (this species only) · gene tree & orthology
Transcription factor family	THAP · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11798 all species →	IMS_HHH	IMS family HHH motif	Motif	Interproscan
PF00817 all species →	IMS	impB/mucB/samB family	Family	Interproscan
PF11799 all species →	IMS_C	impB/mucB/samB family C-terminal domain	Domain	Interproscan
PF00078 all species →	RVT_1	Reverse transcriptase (RNA-dependent DNA polymerase)	Domain	Interproscan
PF00589 all species →	Phage_integrase	Phage integrase family	Family	Interproscan
PF02899 all species →	Phage_int_SAM_1	Phage integrase, N-terminal SAM-like domain	Domain	Interproscan
PF00923 all species →	TAL_FSA	Transaldolase/Fructose-6-phosphate aldolase	Domain	Interproscan
PF05649 all species →	Peptidase_M13_N	Peptidase family M13	Family	Interproscan
PF00158 all species →	Sigma54_activat	Sigma-54 interaction domain	Domain	Interproscan
PF02954 all species →	HTH_8	Bacterial regulatory protein, Fis family	Domain	Interproscan
PF00072 all species →	Response_reg	Response regulator receiver domain	Domain	Interproscan
PF13613 all species →	HTH_Tnp_4	Helix-turn-helix of DDE superfamily endonuclease	Domain	Interproscan
PF05485 all species →	THAP	THAP domain	Domain	Interproscan
PF13359 all species →	DDE_Tnp_4	DDE superfamily endonuclease	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036775 all species →	Homologous_superfamily	DNA polymerase, Y-family, little finger domain superfamily	Interproscan
IPR024728 all species →	Conserved_site	DNA polymerase type-Y, HhH motif	Interproscan
IPR050116 all species →	Family	DNA polymerase type-Y	Interproscan
IPR022880 all species →	Family	DNA polymerase IV	Interproscan
IPR001126 all species →	Domain	UmuC domain	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR017961 all species →	Domain	DNA polymerase, Y-family, little finger domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR006642 all species →	Domain	Rad18, zinc finger UBZ4-type	Interproscan
IPR000477 all species →	Domain	Reverse transcriptase domain	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR037524 all species →	Domain	PA14/GLEYA domain	Interproscan
IPR052387 all species →	Family	Fibrocystin-related protein	Interproscan
IPR018225 all species →	Active_site	Transaldolase, active site	Interproscan
IPR001585 all species →	Family	Transaldolase/Fructose-6-phosphate aldolase	Interproscan
IPR013762 all species →	Homologous_superfamily	Integrase-like, catalytic domain superfamily	Interproscan
IPR002104 all species →	Domain	Integrase, catalytic domain	Interproscan
IPR013785 all species →	Homologous_superfamily	Aldolase-type TIM barrel	Interproscan
IPR004107 all species →	Domain	Integrase, SAM-like, N-terminal	Interproscan
IPR004731 all species →	Family	Transaldolase type 3B/Fructose-6-phosphate aldolase	Interproscan
IPR033919 all species →	Family	Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial	Interproscan
IPR044068 all species →	Domain	Core-binding (CB) domain	Interproscan
IPR011010 all species →	Homologous_superfamily	DNA breaking-rejoining enzyme, catalytic core	Interproscan
IPR042089 all species →	Homologous_superfamily	Peptidase M13, domain 2	Interproscan
IPR000718 all species →	Family	Peptidase M13	Interproscan
IPR024079 all species →	Homologous_superfamily	Metallopeptidase, catalytic domain superfamily	Interproscan
IPR008753 all species →	Domain	Peptidase M13, N-terminal domain	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR002078 all species →	Domain	RNA polymerase sigma factor 54 interaction domain	Interproscan
IPR001789 all species →	Domain	Signal transduction response regulator, receiver domain	Interproscan
IPR025943 all species →	Binding_site	Sigma-54 interaction domain, ATP-binding site 2	Interproscan
IPR002197 all species →	Domain	DNA binding HTH domain, Fis-type	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR025944 all species →	Conserved_site	Sigma-54 interaction domain, conserved site	Interproscan
IPR011006 all species →	Homologous_superfamily	CheY-like superfamily	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR051941 all species →	Family	Blood Group Antigen-Binding Lectin	Interproscan
IPR006585 all species →	Domain	Fucolectin tachylectin-4 pentraxin-1	Interproscan
IPR008979 all species →	Homologous_superfamily	Galactose-binding-like domain superfamily	Interproscan
IPR027805 all species →	Domain	Transposase, Helix-turn-helix domain	Interproscan
IPR006612 all species →	Domain	THAP-type zinc finger	Interproscan
IPR027806 all species →	Domain	Harbinger transposase-derived nuclease domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11076 all species →	DNA REPAIR POLYMERASE UMUC / TRANSFERASE FAMILY MEMBER	Interproscan
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR19446 all species →	REVERSE TRANSCRIPTASES	Interproscan
PTHR46769 all species →	POLYCYSTIC KIDNEY AND HEPATIC DISEASE 1 (AUTOSOMAL RECESSIVE)-LIKE 1	Interproscan
PTHR10683 all species →	TRANSALDOLASE	Interproscan
PTHR11733 all species →	ZINC METALLOPROTEASE FAMILY M13 NEPRILYSIN-RELATED	Interproscan
PTHR32071 all species →	TRANSCRIPTIONAL REGULATORY PROTEIN	Interproscan
PTHR45713 all species →	FTP DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR23080 all species →	THAP DOMAIN PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0042276 all species →	Biological Process	error-prone translesion synthesis	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005975 all species →	Biological Process	carbohydrate metabolic process	Interproscan
GO:0005622 all species →	Cellular Component	intracellular anatomical structure	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0016832 all species →	Molecular Function	aldehyde-lyase activity	Interproscan
GO:0004222 all species →	Molecular Function	metalloendopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0008237 all species →	Molecular Function	metallopeptidase activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0016485 all species →	Biological Process	protein processing	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0008134 all species →	Molecular Function	transcription factor binding	Interproscan
GO:0000160 all species →	Biological Process	phosphorelay signal transduction system	Interproscan
GO:0043565 all species →	Molecular Function	sequence-specific DNA 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
K03511	POLK; DNA polymerase kappa	EC:2.7.7.7	DNA repair and recombination proteins	ko03400	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 →