Gene detail

Detailed information of g16.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: WP_155153587.1, argininosuccinate lyase [Curvivirga aplysinae]
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
A3PMB7	Argininosuccinate lyase OS=Cereibacter sphaeroides (strain ATCC 17029 / ATH 2.4.9) OX=349101 GN=argH PE=3 SV=1
Q3IZY2	Argininosuccinate lyase OS=Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) OX=272943 GN=argH PE=3 SV=1
Q8U9X6	Argininosuccinate lyase 1 OS=Agrobacterium fabrum (strain C58 / ATCC 33970) OX=176299 GN=argH1 PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000111 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000574 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001327 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001564 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002710 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003149 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0012037 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0016121 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0021338 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02668 all species →	TauD	Taurine catabolism dioxygenase TauD, TfdA family	Domain	Interproscan
PF00206 all species →	Lyase_1	Lyase	Domain	Interproscan
PF14698 all species →	ASL_C2	Argininosuccinate lyase C-terminal	Domain	Interproscan
PF00084 all species →	Sushi	Sushi repeat (SCR repeat)	Domain	Interproscan
PF07699 all species →	Ephrin_rec_like	Tyrosine-protein kinase ephrin type A/B receptor-like	Domain	Interproscan
PF02494 all species →	HYR	HYR domain	Domain	Interproscan
PF01477 all species →	PLAT	PLAT/LH2 domain	Domain	Interproscan
PF01039 all species →	Carboxyl_trans	Carboxyl transferase domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050411 all species →	Family	Alpha-ketoglutarate-dependent hydroxylases	Interproscan
IPR042098 all species →	Homologous_superfamily	Taurine dioxygenase TauD-like superfamily	Interproscan
IPR003819 all species →	Domain	TauD/TfdA-like domain	Interproscan
IPR008948 all species →	Homologous_superfamily	L-Aspartase-like	Interproscan
IPR022761 all species →	Domain	Fumarate lyase, N-terminal	Interproscan
IPR009049 all species →	Family	Argininosuccinate lyase	Interproscan
IPR029419 all species →	Domain	Argininosuccinate lyase, C-terminal	Interproscan
IPR000362 all species →	Family	Fumarate lyase family	Interproscan
IPR024083 all species →	Homologous_superfamily	Fumarase/histidase, N-terminal	Interproscan
IPR020557 all species →	Conserved_site	Fumarate lyase, conserved site	Interproscan
IPR003410 all species →	Domain	HYR domain	Interproscan
IPR043555 all species →	Family	Sushi repeat-containing protein SRPX-like	Interproscan
IPR000436 all species →	Domain	Sushi/SCR/CCP domain	Interproscan
IPR011641 all species →	Domain	Tyrosine-protein kinase ephrin type A/B receptor-like	Interproscan
IPR035976 all species →	Homologous_superfamily	Sushi/SCR/CCP superfamily	Interproscan
IPR036392 all species →	Homologous_superfamily	PLAT/LH2 domain superfamily	Interproscan
IPR001024 all species →	Domain	PLAT/LH2 domain	Interproscan
IPR008979 all species →	Homologous_superfamily	Galactose-binding-like domain superfamily	Interproscan
IPR006585 all species →	Domain	Fucolectin tachylectin-4 pentraxin-1	Interproscan
IPR051941 all species →	Family	Blood Group Antigen-Binding Lectin	Interproscan
IPR011762 all species →	Domain	Acetyl-coenzyme A carboxyltransferase, N-terminal	Interproscan
IPR029045 all species →	Homologous_superfamily	ClpP/crotonase-like domain superfamily	Interproscan
IPR011763 all species →	Domain	Acetyl-coenzyme A carboxyltransferase, C-terminal	Interproscan
IPR034733 all species →	Domain	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Interproscan
IPR045190 all species →	Family	Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10696 all species →	GAMMA-BUTYROBETAINE HYDROXYLASE-RELATED	Interproscan
PTHR43814 all species →	ARGININOSUCCINATE LYASE	Interproscan
PTHR46343 all species →	HYR DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR33332 all species →	REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR45713 all species →	FTP DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR22855 all species →	ACETYL, PROPIONYL, PYRUVATE, AND GLUTACONYL CARBOXYLASE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0004056 all species →	Molecular Function	argininosuccinate lyase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0042450 all species →	Biological Process	arginine biosynthetic process via ornithine	Interproscan
GO:0062023 all species →	Cellular Component	collagen-containing extracellular matrix	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0016874 all species →	Molecular Function	ligase activity	Interproscan
GO:0004485 all species →	Molecular Function	methylcrotonoyl-CoA carboxylase activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006552 all species →	Biological Process	L-leucine catabolic process	Interproscan
GO:1905202 all species →	Cellular Component	methylcrotonoyl-CoA carboxylase complex	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
K01755	argH, ASL; argininosuccinate lyase	EC:4.3.2.1	Exosome	ko04147	deepkoala
K01969	MCCC2, accD1; 3-methylcrotonyl-CoA carboxylase beta subunit	EC:6.4.1.4	Valine, leucine and isoleucine degradation	ko00280	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 →