Gene detail

Detailed information of KAL9984635.1 in Oculina patagonica

Genomic Location: chr2:30899665...30904913
NR annotation: KAJ7391590.1, hypothetical protein OS493_017287 [Desmophyllum pertusum]
Species Oculina patagonica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-ACROYT_G006954.t0

AAACACGACTGTGCCGGCAGTTGCAATCAATGGCGAACACGACGGTTCTTATCATTTTGGCCGATGTGGTTGGCTGGAGTTATTTCTTATGTTGGACAGTATCCTTTTTCCCGCAGATATACGAAAACTGGAGACGGAAATGTGTGGTGGGCTTTTCGTTCGATATGTTGGGCTATTTTCTCCTCAGTTATGTAACATACCTGATTTACAATGTGGCGGTGTACTTCGACCCGAAGCTAGTTCTGAGCGATCTGAACGAGGACAACCCTGTGAAGTTAACGGATGTAGTGTTCGCTATCGTAGCGTTTATATGTACGAGTTTTCAGGGAATACAGTGCTTGATGTATGATCGAGGATCACAGACAATTCATCGTAGCACTGTCGTTGTTTGTATTGGTTGTTTGCTTGCTCTGGCCGTGCTAACTGTTCTTCGCTGTTTTGGGGTCGGCTCGTGGTTTTTGGTCCTCCAGTACTGTGGATACGTAAAACTGGTTGTGTCATTCGGAACGTATTCTCCTCAAGTGTGGCTTAATTTCAAACGCAAGTCCACAGCTGGATTCCATATTGGTGGAGTGTTGCTTGATTTTGGAGGTGGAGTTCTTAGCTTGCTACAAATGGATCTGTACTGCTTCATCGAACACAGTAACACTCAGCTGACTGGCAACATTCCCAAGATGGCCTTGGCTGTCGTCACACTCTTATTCAACATCATCCTTGTCTGGCAGCATTATGTTTTCTACTTTGGAAACGAACACGATGCTAGTGAACAAGAACCACTATTGAAAGGTAGGAAGAAGACTAAGTTTTATGCTGTAGATGTCAACGCTGATGATGGAGATTTACTGGTGACGAGTTTGTCTCTGTCAATGGAACAAAGTGCTGAAGAGGTGAGACGAACTCATTCGCAAGAGTCCCCCGTGTAAACTTATCAGTGGACTGTCAATCAGATACACACTATACtggtaattattttaatttattgagtGGAGGGATTCAGATTTGGtaatttaaactaaaataatttaatttgtttatttattaatccTATTAACTAATTTAAATTATGGAATTGCTGTTATCAGTCAACTTGTGGAAATATATGCAAaatatgaaaattatttaaaacatttcaactACCGGTAGCCCATGTGAGTGACCATATTGTAATCTGTCAAACTTCAAAATTGAGACTATACAATGTACTGTACATGCAGATTAACcaagaatatatttttaaatgcaGTCCTTCTACATGTACgtgtacatgtaatataaaaaGCTGTTCTTATGGACACTGTTTATATAGTTAACTTTTGCTCATGGGCTTGCTTGACTTGTCATGCCATAGACAACACTGTAGTGAGAATTTAATGGAAAAATTTGAAACCAAAGCTTTAAAAGTCTatattttataaaatcaaacaaataGCAAATGAAGGCAATTATATTGCTATAAAGAATTTATATATGTTATAACATATTGTTATAAAACAATAGATAGGTATTTTTGCCCAGGTGATGTTGTAAGCCATTTgagaggtacatgtacatgtatgttaatttttaattttcaattgtCTACTAAATCCTTGAAGTACAGTTATCTTGTATGAAAGTGAGATAACCAAAAAAGGAAtaattcaataataataatgataataattctTTATTGGAAGAAACTTATTACAACACACAGGCACAGGGTTTTTGGGGCGatctttcataaaaaaatataaataaataaattaaatttaatttgataaGATTTTCTCAGTAACAGCTGGTAAAGGTTTaatatttatttgtaaaataaatatattaataatGTAAGTTTGAAATGCTTGGTTTAAATTTCAAGTTTGAAATGGCTGTTTGAAtatgcaaccctccaagttaagaccattttagtcgccatggcgactaacattttggagctggcgactataTTGGAaccaaaattgagaagaaggattgaaagcatgagcttaatttagcgactaaaatttttcactggcgaccagtcagtggccaaatggccactgtcaaaaaaaataaacttggagggttgatatgTGCTTAAGTTATTAAAATAGTTGGGAGTTTTAAGGTTTGGGTAGTAATAAGTTAATTAAGGAAGATATGTCACAATATTAAGCCTTTTTTTGCTGTGTACTAGCTTGCGAACACAGTCGCATTTCCAGCTTTCGCTTGTCTCTGCCGGAAAATGAGAGAGACAGGCAAAAGCTGGAATTGTGTCTGCTTTTGCAggctagctgtaagaagaattACCTCCTAATTGattaaataagttaaaaataagacaaaaatgGTCAAGGATGGTTAAAATTGCAAATGATTATGACTAATTAAGGTTCACCATCCATAGCATAGTGCTACATTTAGTGAAATTTAAATTAGGCAAGACTGCCTTGAAAATgctatatgtacatgtatgtattctATAATGCATTTAAAATTGCATTACAGTTATTTTACTTTCTAATTTACTTTTAAGAACACTTGAGTATCAAACATACTTTACCTATTAATAGCACTGAAAGGCTTCTTGAGGTGGACAGTGTTAGGAGATGATAAAAAATGAAGCCCACTAATTTgtaaaagaaagagaaaagagGGATTCTTAAATCCTCAATTTCAGTCTGTTAAGAGTGATATTTTGAAATcgaatttgttttaaatcatttttaaaagaacGTTTTGTAAATAGTCTATAAATCCTGTGTGAGTTTATGACtgaacgaatgaatggatggatggatgaatgaatgactgaatgaatgaatgaatgaatgaatgaatgaatctgTATTTATTCCACACAGTTGCAACATCGTGCAATTTTACATTACAGACAATTTTAAAGTTACTAAATATTATCAAAGCTAATGTTAAGATCAAAAGCACACTATAGACCTAGTTCTATACTTATTGAAACAAACATCTATCACTTCAGGCAATTAAAGTTGGTTTACCTTTTAAGAATTTGTTTAATGTTTCCGCTTCAACTGAACATTAGCTTTGCCTTTTACAAGAAATGTCCTCCTTCCAAATATGCTTGAAGAAGGAATGGAATAAAAGAATCTCCTTGGGCCTTAATTGATGATTTACGGTTGTG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q54WT7	Cystinosin homolog OS=Dictyostelium discoideum OX=44689 GN=ctns PE=3 SV=1
Q9VCR7	Cystinosin OS=Drosophila melanogaster OX=7227 GN=Ctns PE=1 SV=2
A7MB63	Cystinosin OS=Bos taurus OX=9913 GN=CTNS PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002152 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04193 all species →	PQ-loop	PQ loop repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006603 all species →	Repeat	PQ-loop repeat	Interproscan
IPR005282 all species →	Family	Lysosomal cystine transporter	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13131 all species →	CYSTINOSIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005774 all species →	Cellular Component	vacuolar membrane	Interproscan
GO:0015184 all species →	Molecular Function	L-cystine transmembrane transporter activity	Interproscan
GO:0015811 all species →	Biological Process	L-cystine transport	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
K12386	CTNS; cystinosin	-	Exosome	ko04147	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 Oculina patagonica 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 Oculina patagonica, 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.

Dataset	Tissue / stage	Cells	Cell types	This gene	Marker of
OPATA_whole_adult	Whole adults · Adult tissues/organs	21,775	31	not in this dataset	–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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 →