Gene detail

Detailed information of XP_068732825.1 in Montipora capricornis

Genomic Location: chr13:32465254...32482309
NR annotation: XP_015753584.1, PREDICTED: cyclic nucleotide-gated cation channel alpha-3-like isoform X1 [Acropora digitifera]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068876724.1

GTTTTTGTCAAAGAGTTGAGCCCCAAAGCCAGACAAACTTCGTTTAAAATTTTACAGATTTGTCATCAGATTCGCCAAACCTGACTCATCAAAGACCCTCAGTGGCGCTGAAAACAAAGATGAATGAAGGAACAAGTAGAACATCAAGAGTCCGCTTCTCAGCTAATACAGATGCTTTcagcgaagaagaagaagcggATATTCGGCACAAACGCTTACTTCGCTATTGGTACAAAGGTGGACGAAGATACAGCGAAGCCGAAAAAGCGTTTTTAAGCCGTGTCAGGATACCCTCTGTTGGACTCATTGCTGATGGTGAAACTAAAGTTGGATGGCTTCGATTTTTTGATCCGGGAGGTGACAGACTGTATTACTGGTTGATGATTGTCTCCATTGCAGTTGTTTATAATTCATGGGTGCTAATATTACGAAGTTCATTTCCGGAAATTCACAAAAGACATGAGATCATCTGGATGACCATAGACTATTTGTGCGAtattatttatattcttgacTTATTTGTCAGTTCACGGACGGGTTATATGGAAGACGGTATTATGCAAAAAGACATTCAAAAAATGCGGCGACATTACTTACGTACATCAGCGTTTTATTTGGACGCAGCCTCAATCATACCGCTGGACATTCTGTACATTTTCATCGAGCGCGAGCCCGCAGTACGCATGAATCGCCTGATAAAGTACCACCGTTTCTGGAGATTTCTTGATCGCACAGAGAGCCGGACCAGTTACCCGAACATGTTTAGACTGGCCTCCCTGATGCAGTTCATTCTTGTGATAATTCATTGGAACGCTTGTATATATTTCATAGTATCTAGAAACATTGGGTTCGGTACAGACAATTGGGTGTACCCGGGAATCATCGGTAACTTAAATGCAACGCACGAGTCACTCACACGGAAATACATTTATTCTTTTTATTGGTCAACTCTAACGCTGACCACCATTGGGGAAGTACCGCCACCTCACACAAATGTGGAATTTATCATTGTAACTCTCGATTACTTAATAGGAGTCCTTTTATTTGCTACCATCGTTGGAAACGTTGGTAATATTGTCACGAACCAAAACGCTGGCAAAGTGGACTTTCAAAACAAGATGGACGGGATTAAAGCCTACATGCGTTTTCATAAGATCCCGCAGCATTTACAGCAGAGAGTAATCAAATGGTTCGATTACTTGTGGATGAACAAAAAGCACCCGGATGAGGAAGAGCTTCTCCGTTCTTTACCGGACAAACTCCGGGCAGAATTAGCCATTCATGTACACTTGGATTCATTAAGAAAGGTCGCCATCTTTCAAGATTGTGAGGCGGGGTTTTTGAGCGAGCTGGTCTTGCGACTTCGTGCTCAGCTTTTTTCACCAGGGGATTACGTCTGCAGGAAAGGCGAAGTGGGTCGAGAAATGTACATTGTTAATAGGGGCAAGTTAGAGGTGGTATCAGAGACGGGCACCAAAGTCTATGCCGTGTTAGAGGCCGGAAGTTACTTCGGCGAAATTAGTGTGTTATGTATGAGCGCCGCTGGAAATCGTCGGACCGCCTCGGTGCGCTCCGTTGGCTACTCAGAGTTATTTTGCTTGTCAAAACACGATCTCATGGAAGTGCTCGATGAATATCCCGAGATCAAGACGAAAATTGAGAGCATCGCAAAACAACGACTGGAGAACGACAAGAAACGGACAAGCACGTTGCTGACAAACAAACACACGAGAACTGAAGAAAACTGCGCTGACAGTGAACCGAGGCCAGTTAAGAGCAGAACTTTCGCCAAGATGGAAGATAGGATTGCTACACTTGAAAGGGATAGAGATAAGCTTATAGAAGAGTTAAAAAGACAAAGAGAAGAGTTTTTAAACAGACTCGCTGATCTTGAGTGTTCAATGTCACACCTATCAAGGGAACGACGAGGCGAAGGAACACATAGACCCACTTCAAGATCTTTTGACTTCGTTTGGaaaagaagataattttactGCCATTTTGAATCACTTCTCTGGAGCAGGAAAACGTGGTTTACAGTATTGCCTTGAGTTGCGGACGTGTGAGACATTTTCTGCCCATGTGCAACCGTATCACTTTGTGTTTCGCAAGTGTGATGCATTTTAATTCAATCCAGTCGGTACTGCTCGTACCGCTTTTCCTGTGATCTAGTTGTCTGCACTCTAATATTCCGGGCATTGCTTCCTTAACGTGACGGCAAATGGAGAACTTTTGGATCCTTTTGTCTATCACTGATGtggtaaacaaagaaaattgagtTTAAAACCGGCCACGTTCACCCTACccttggttttcatccacgtgatgagacggccatcttggtgtacaaaacaatagaaaatggttccacaagttttgcatcagaatagagtcaaattcccaggagacattttactgcattgttctctacaccaacatggccgccgtgacgtcagatgaaaactcCCAACAGGCATTGCATGAAAATCCcgtcaaagctgaaattcatccaatcagatcgctacgataagcaatgcccaaaaggccatttccgagttgatgtTTGTCTCGggttcaaagcgagtcttggtgattttcataagaatacgcaactcattttcatttgaatggttgtgcaccgggtcccgctttgaaactgaggcatgcagcaactcggaaatggattatttccataacaaaaacacatggtcgaaaagcctgtcgttTGAAGGTGGACCTTTAATAGAACGTGGTTTGAACCGAGGAGTTTCATACCTCAATGGAATTTGATTGTTCCGGTGAAAAGAGCCGTGAGAAGGATTGTTGgcagtgactgacgtttcaacaACCTTAGCGGGAATCACCTTCACGCAGAGTCAAGTGATGATTGGAAATTCAAACGGATATAGTGATGCTCTGGTCTGTGTTTGTGATTGGTAGTTGGAAaagtaatgtgattggttgtGATGATGGTTAGTGGTagtagttgagacagttgcaacagagcacactggcaacgacacattcattgtttgcaaagaaaacctGTCCAAAAAGTACTTTTCCGTGATACCCCTCCCTctccaccctaatcaatgttgtaccgctggcGACAAGGCTCcgcgtagaaaacagaaaaaaacacaacattgtcccgggggtgcagGGGAGGGGGCCCTTTTCGCACCGAGCTTgagataagagtgtctcaacaattttgacgccgattgcaGAAACAAAACATTGTCCAAAGGTCAACCCAATTTGCCAAAACACAAGTGGTGATGAAgattttaaaacgtttattgAAAGACCTGAATTTGAGACACAGATTTGCCCAAGCCCATGATGCTGTTACGTATAAGATATGTATAAAGTGTATAAATATATGTATCACCTGTGTAACTCAGTCATACGTTATGTGAGTAGATACGTTCAATTATACATTCTCTAGGATATTTCAATCGAACCAACAACGCCAGCCCACGCATCGGCAGTTTTGCGTGATGGTTGCTTgttcttaaaataaaaatgaaaaattcaatGGCTAATAAGGCCTGGTGCCATGTTCGAAGATAAGTTTTTTTAAGCTTTCTAATTTTGCTGAATGAACATTAAATGATTGCCTGCCATGACCTGGCATGTAAACCTTGTCATCAATGCTCAACACAATTGATTAACGTTGCTCTTTAAGTGTACCAACATTCGGCGTATCCATTCTTCATACAAGAAACTGAGGATGTTTTAAGGGGGAGTTCGCTGATGGCTAGTGCAAGAGAATACTAGCACTTCTGAAGAACACTAATACAACACTTAAACTTCAAACAAAATTCGCAAGTTACGCAAATTCGAAAATAGAATAAGCGCAATTGCCTATAGGCAAGCTTTCGCAAATTCATCTGAAACAGGGAATCTATAAAAACATAATTTcaatcatagttaatcgagggactggttatgaaaccttagaactttcaaaagcgagaacaatgttgttgcaatcggtgttgaattgaccgtgaccctgcacaatcttttgttttcgcttcgcacgggttcgcaaattagttgcgcataatttaatcgaaggatttgattggttatcttctcgaaaaaaggtgcaGCTTTTCTTGCCTCAGTAGATTACCTTAGAGAATCATCACATCTCCTTTTGAGAACCGATTTTAGATGACTGTAATCATAACAATGAAGATTCTTTTCTTCATCCTCATCGtaatcatcatcttcatcgttATTGTTGGGTTAAACATAAAAAAGCCGGCCTATAACATTACACCTTTGAGTGTTGTGATAAATCAAACTAATAATTAATTGAATAAGCTTCACAATTTTATTACCCATTTTCTCTTTGCACCTATGATAACATGTCACCATCTTTCACCAAGATATTCAGTAATTTAATGAACGTATTTGtatacttatttttattttacaccTTTATACATCGTCAAAGCTATCTACAACACAAACGATGAACTGCTAGTAATTCCCCAACCCCCGGCTATAAACGTGATATCAATTCAATATAAGAACTCTTTATTTACAGTAATAAGCTAAAGGATgaaatttaaaatcaaaatgctgATGACGCTATGTTGTTCTTGGTTAAGATTGATTTGATTGCTTTGGCCCACTCGCGGTCTCTTAGACGCTTTGAGAAAGTTCTGACCAACCTATTTGTCCACAAACGAGCTCGCTATTACTCCTTTGCTTTCTCAGATAGGGGTGAAACAGCAGCATTTATTTAGCCTCAATGAAAGCGAGGATCGGCGAAGGGCAATAAAGAACACCTCATCGCAGGTAAAGGTTCAGTGAGAATCCAATGAAAAGTATACTTACAATTATCAAGCACTGTTCTCTCAAAGCATGACAACAgatttaaatttgaaatttgagtaAAAATTTAAGCTTTGCTTTGTTCCATTTGCAAACACTTGGTATCCACAATGCACCAGATGGAAGGATAATTAGATGTAAGCttagaccaaaaaaaaaaattgttattttagtTTCGAGGTATCACCTCATCTAGTCCTAATACAGCGTACCTAATTGCTCAAAATTGCTGGTGCATAACTGTACTGAGATCTCACAGGCCGGCTTGGTATTCCATGATGCATTGCGGCTTGCATGTCAACGAATTCCTCCAATACATCCGGATAATACCTTTCACTGGGACCTCCGCTAACTCCTGAGATCGGATACATAGTATTTGAGGCCACAGCGCTTGCAGGGAACATGTAGGATGAAGGGTAGCTTCTTTCATTCGGTGGGTACTGTGAGTAATGCTTGAATTGATCAATTGGAGATACACCTCTGTACTCGTAGCCTGGAATGTTGGGAGCAGGCGTCATGACCGCGTAGCTTGAATCGGCCATGCTGTTTTTGGAGCGAACTATAGTGTAACTTGTTCC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q03041	Cyclic nucleotide-gated channel alpha-2 OS=Bos taurus OX=9913 GN=CNGA2 PE=1 SV=1
Q16281	Cyclic nucleotide-gated channel alpha-3 OS=Homo sapiens OX=9606 GN=CNGA3 PE=1 SV=2
Q29441	Cyclic nucleotide-gated channel alpha-3 OS=Bos taurus OX=9913 GN=CNGA3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000737 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00520 all species →	Ion_trans	Ion transport protein	Family	Interproscan
PF00027 all species →	cNMP_binding	Cyclic nucleotide-binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000595 all species →	Domain	Cyclic nucleotide-binding domain	Interproscan
IPR005821 all species →	Domain	Ion transport domain	Interproscan
IPR018490 all species →	Homologous_superfamily	Cyclic nucleotide-binding domain superfamily	Interproscan
IPR014710 all species →	Homologous_superfamily	RmlC-like jelly roll fold	Interproscan
IPR050866 all species →	Family	Cyclic Nucleotide-Gated Cation Channel	Interproscan
IPR018488 all species →	Conserved_site	Cyclic nucleotide-binding, conserved site	Interproscan
IPR003938 all species →	Family	Potassium channel, voltage-dependent, EAG/ELK/ERG	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45638 all species →	CYCLIC NUCLEOTIDE-GATED CATION CHANNEL SUBUNIT A	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005216 all species →	Molecular Function	monoatomic ion channel activity	Interproscan
GO:0006811 all species →	Biological Process	monoatomic ion transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0005223 all species →	Molecular Function	intracellularly cGMP-activated cation channel activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0017071 all species →	Cellular Component	intracellular cyclic nucleotide activated cation channel complex	Interproscan
GO:0044877 all species →	Molecular Function	protein-containing complex binding	Interproscan
GO:0098655 all species →	Biological Process	monoatomic cation transmembrane transport	Interproscan
GO:0005249 all species →	Molecular Function	voltage-gated potassium channel activity	Interproscan
GO:0006813 all species →	Biological Process	potassium ion 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

No KEGG orthology assignment for XP_068732825.1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of XP_068732825.1 across 36 RNA-seq samples of Montipora capricornis. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

36Samples

30TPM > 0

1Conditions

28.8Max TPM

4.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	4.56	28.83

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	28.83
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	9.10
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	8.86
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	8.72
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	7.87
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	7.11
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	7.04
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	6.80
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	6.75
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	5.84
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	5.79
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	4.96
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	4.47
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	4.43
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	4.40
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	4.07
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	3.79
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	3.57
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	3.52
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	3.00
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	2.90
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	2.78
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	2.77
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	2.70
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	2.63
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	2.56
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	2.46
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	2.42
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	2.20
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	1.88
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora capricornis 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	29	XP_068746209.1	0.982403764737463
Negatively correlated	3	XP_068724527.1	-0.281351848739141

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora capricornis, 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.	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.	ready	open →
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 →