Gene detail

Detailed information of g7239.t1 in Acropora digitifera

Genomic Location: chr3Alt:28628294...28639938
NR annotation: XP_029203760.2, alpha-dioxygenase 2-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g7239.t1

ATGGATCCTGGGCTGCGTTACCTGATTGGACTTGTTTTCTATGGACTTAAGCAAGTTAAGGTGTGGTGGCACCTGCCTCTGGTCTTGACAATGACCTATACGTTCTATGTACGAGAACGACTCCTAAATAACTCCCTCTTTGACGCATATCCAAACCCTCTGCCTCAGGCCAAGCGCCGTTGTAATGACCCAGTATTAGGTGACGGCTACATTGGTTGCTTTTCTGCGTCTCTCATTTCTGATTACAAATTCCAGATGCAACTTCTTACGCCTTCAGTTACACCAGACAACTGCATTGCACAATGCAAAACTGCAATGTTTTCTTATGCAGCATTAGGACAGGGTCAAAGGTGCTACTGTGGCGTGGGATATGAGTCAAAGAAATATGCTGATGAATGCAATTGCCGAAAAAAGTGCAAAGGAAACAAAAAGAACAGATGTGGGGGGTCGCATCACGTCTCCCTTTATAACACCTATATTTGCACGGACAGAATGAAAACGATGCGAACAATTGATGGGAGTTGCAATGACCTCAACAATACGGCTGCTGGAAGCAGGTTTTACCGATTTGGCAGAAATGTTCCTTTGCAATATGCCTACAGCAAACCTCAAGATCTCCTGAAACCCGATCCGCGAGTTGTAGCGAGAAAACTATTGCAGCGTCAGAAGTTTTTGGAAGTTCCTTGGTTGAATCTCTTCGCGGTGGCCTGGGTCCAGTTTATGGCGCATGACTGGTTTGACCATGGTACTCCAGTCAGAGAGATGCCGATCAAAATTCAACTGGAAAAGAAGGACCCTCTTAAAAAAAGACTGAGAGGTGTCATGAAAGTCGACCGTACCAAACCAGACAAATGCCGAGTTCAAGGTGATTCTGTGCCCCCAGCTTATCAGAATGACGTCACACACTGGTGGGATGGCTCACAGCTGTATGGCAGTGATGAATATACGCATGCGCGAGTTCGGTCTTTTGTTGATGGCAAACTGAAAGTTGACGACGATGGATTTCTTCCTTTGGACCCCAAAACTAAAATCGATATTTCAGGATTCACAAAAAACTGGTGGGTTGGACTTAGTCTCCTGCACAACTTATTTACCAGAGAGCACAATGCAATTTGTGATATGCTGCGGCAGAAACATCCTAGTTGGATGGACGATAAACTGTTTCAAACTGCAAGGCTCATCAACACGGCTCAAATCGTCCAGATACATACGCTGGAGTGGACTGGTGCAATACTGAACACGGATTTTATCCATGAGTCTCAGATAGGGCAGTGGAATGGAACGTTAAGTGGAAAAGTGAAGGAAATCCTAAAACAAATGAACGTTACGCTGGGGAAGGGCAGCATCCCCACCCACAGAGGAAACTTGCCTGACTACCGTGGAGTTCCTTTCTCTTTGACGGAGGAATTTGTTTCTGTCTATCGTATGCACTCGCTGTTGCCAGACATCATTTCTTTGCGCTGTATGGGAAAAGACAAACTTAATGGGCGAACATACAGTCTTCCAAATTTTTCATTTGGGGAAGCTCGCAAAATGTTTGACGAGAACGATCTAGGTGACATCCTGTACACATTTGGAGTGGGTAAAGCGGGCCAGCTTGTGCTACACAACTACCCTACGACTCTGATGGAACTGAAAATTCCAAAGAGCCAAACTGGGGGACCTGCGCCTATTGATCTTGCCACCATAGATATTCTAAGGGACCGCGAAAGAGGTATCCCACGGTATAACCAATTCAGACGCTTGCTAAACCTCACAGCACCAAGCACGTTTGAAGAGCTTACTAACGACACCGTCACAGCTGCAGAACTCAGGGATGCATACAAAAATCAAATAGAGGATGTGGACCTTTTGATTGGCTCTCTAGCTGAAGCGCGTCCTAAGGGATTCGGGTTTGGCGGCACACCATTTCATCTCTTCTTGTGCATGGCGAACCGCCGTCTAAACACAGACCGATTTTTAACAATTGACTACAAAGAAGAATACTACACCAAAGAGGGACTGCAGTGGGTCGAGAGATCAACATTCAAGCGCGTTCTGCTTCGTAACTTCGCTAATGTGAAAGGCTTATCCAAAGCCTTGCAAAAGGTTGACAACGCCTTCTTTGTGTGGGACAAAAAGTAA

Transcript

chr3Alt.g7239.t1

TGAAGTATTGCTGTTGCAACTCCAAGCAATTACTATTTCGCGCTCACTGATTCCAGTTAATTCTTATTCGCGTTGAAAGCGAGGCTTGGAGGTGAGACGAGAGCGTCTTAAGTAATCATACGACGTTCTCCATTTCTAGGTTGAATACAGTTGCTTATCTCAGGCTTCGGATTGGGGGCTATCTGTTTTGAATATTCAAGCCTCGAGGCTTCGTTGTTGAACTGTTGTACACAGTTCCGTTTTGTGACTCTCAACAGAGGGGACCCTTGATTGTTCCTACAATGGATCCTGGGCTGCGTTACCTGATTGGACTTGTTTTCTATGGACTTAAGCAAGTTAAGGTGTGGTGGCACCTGCCTCTGGTCTTGACAATGACCTATACGTTCTATGTACGAGAACGACTCCTAAATAACTCCCTCTTTGACGCATATCCAAACCCTCTGCCTCAGGCCAAGCGCCGTTGTAATGACCCAGTATTAGGTGACGGCTACATTGGTTGCTTTTCTGCGTCTCTCATTTCTGATTACAAATTCCAGATGCAACTTCTTACGCCTTCAGTTACACCAGACAACTGCATTGCACAATGCAAAACTGCAATGTTTTCTTATGCAGCATTAGGACAGGGTCAAAGGTGCTACTGTGGCGTGGGATATGAGTCAAAGAAATATGCTGATGAATGCAATTGCCGAAAAAAGTGCAAAGGAAACAAAAAGAACAGATGTGGGGGGTCGCATCACGTCTCCCTTTATAACACCTATATTTGCACGGACAGAATGAAAACGATGCGAACAATTGATGGGAGTTGCAATGACCTCAACAATACGGCTGCTGGAAGCAGGTTTTACCGATTTGGCAGAAATGTTCCTTTGCAATATGCCTACAGCAAACCTCAAGATCTCCTGAAACCCGATCCGCGAGTTGTAGCGAGAAAACTATTGCAGCGTCAGAAGTTTTTGGAAGTTCCTTGGTTGAATCTCTTCGCGGTGGCCTGGGTCCAGTTTATGGCGCATGACTGGTTTGACCATGGTACTCCAGTCAGAGAGATGCCGATCAAAATTCAACTGGAAAAGAAGGACCCTCTTAAAAAAAGACTGAGAGGTGTCATGAAAGTCGACCGTACCAAACCAGACAAATGCCGAGTTCAAGGTGATTCTGTGCCCCCAGCTTATCAGAATGACGTCACACACTGGTGGGATGGCTCACAGCTGTATGGCAGTGATGAATATACGCATGCGCGAGTTCGGTCTTTTGTTGATGGCAAACTGAAAGTTGACGACGATGGATTTCTTCCTTTGGACCCCAAAACTAAAATCGATATTTCAGGATTCACAAAAAACTGGTGGGTTGGACTTAGTCTCCTGCACAACTTATTTACCAGAGAGCACAATGCAATTTGTGATATGCTGCGGCAGAAACATCCTAGTTGGATGGACGATAAACTGTTTCAAACTGCAAGGCTCATCAACACGGCTCAAATCGTCCAGATACATACGCTGGAGTGGACTGGTGCAATACTGAACACGGATTTTATCCATGAGTCTCAGATAGGGCAGTGGAATGGAACGTTAAGTGGAAAAGTGAAGGAAATCCTAAAACAAATGAACGTTACGCTGGGGAAGGGCAGCATCCCCACCCACAGAGGAAACTTGCCTGACTACCGTGGAGTTCCTTTCTCTTTGACGGAGGAATTTGTTTCTGTCTATCGTATGCACTCGCTGTTGCCAGACATCATTTCTTTGCGCTGTATGGGAAAAGACAAACTTAATGGGCGAACATACAGTCTTCCAAATTTTTCATTTGGGGAAGCTCGCAAAATGTTTGACGAGAACGATCTAGGTGACATCCTGTACACATTTGGAGTGGGTAAAGCGGGCCAGCTTGTGCTACACAACTACCCTACGACTCTGATGGAACTGAAAATTCCAAAGAGCCAAACTGGGGGACCTGCGCCTATTGATCTTGCCACCATAGATATTCTAAGGGACCGCGAAAGAGGTATCCCACGGTATAACCAATTCAGACGCTTGCTAAACCTCACAGCACCAAGCACGTTTGAAGAGCTTACTAACGACACCGTCACAGCTGCAGAACTCAGGGATGCATACAAAAATCAAATAGAGGATGTGGACCTTTTGATTGGCTCTCTAGCTGAAGCGCGTCCTAAGGGATTCGGGTTTGGCGGCACACCATTTCATCTCTTCTTGTGCATGGCGAACCGCCGTCTAAACACAGACCGATTTTTAACAATTGACTACAAAGAAGAATACTACACCAAAGAGGGACTGCAGTGGGTCGAGAGATCAACATTCAAGCGCGTTCTGCTTCGTAACTTCGCTAATGTGAAAGGCTTATCCAAAGCCTTGCAAAAGGTTGACAACGCCTTCTTTGTGTGGGACAAAAAGTAAAATGACTGTTGCCGAGATCACGAGTAGCATTTTCGCAAATGCTGAAAAGTTCAACGTGAAATAGAAACCGTTCCCTATCCCTGGAATTGTCTGGGGTTTTTTTTGTTTGTTTTTTGTCATTAACAGAATCCACCTGTTTGGTGTTTACCTTTAGCCAAAAATGCGAACTGTTATCTCGAATTTTAAGTCAATCTTTTGTTTCTTTAACTTTTCTGCCTCATTCAAAATACTATTAGCTTGTGAAAAAAAGAAACCTGTATACTAAATGAAACATCATTTTGCTTACTTTCCGCCTATTACGCCTTCGTGTTTAGTTCGTATTTTGTCAGAAAGGGTAGATAGACTAAGTAACTTTGAATTGAGTAAATCATTGTATGGTGTTGTCTTGATGCTAGTAAACATGTACAATAAAGTTAAAATTAATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q2QRV3	Alpha-dioxygenase PIOX OS=Oryza sativa subsp. japonica OX=39947 GN=PIOX PE=1 SV=2
A0A2G3AC72	Alpha-dioxygenase 1 OS=Capsicum annuum OX=4072 GN=T459_06886 PE=2 SV=1
Q9C9U3	Alpha-dioxygenase 2 OS=Arabidopsis thaliana OX=3702 GN=DOX2 PE=2 SV=1

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01822 all species →	WSC	WSC domain	Domain	Interproscan
PF03098 all species →	An_peroxidase	Animal haem peroxidase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002889 all species →	Domain	Carbohydrate-binding WSC	Interproscan
IPR034815 all species →	Family	Alpha-dioxygenase	Interproscan
IPR037120 all species →	Homologous_superfamily	Haem peroxidase domain superfamily, animal type	Interproscan
IPR019791 all species →	Family	Haem peroxidase, animal-type	Interproscan
IPR010255 all species →	Homologous_superfamily	Haem peroxidase superfamily	Interproscan
IPR050783 all species →	Family	Oxylipin biosynthesis and metabolism	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11903 all species →	PROSTAGLANDIN G/H SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0004601 all species →	Molecular Function	peroxidase activity	Interproscan
GO:0006979 all species →	Biological Process	response to oxidative stress	Interproscan
GO:0020037 all species →	Molecular Function	heme binding	Interproscan
GO:0004666 all species →	Molecular Function	prostaglandin-endoperoxide synthase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0016702 all species →	Molecular Function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	Interproscan
GO:0019371 all species →	Biological Process	cyclooxygenase pathway	Interproscan
GO:0043005 all species →	Cellular Component	neuron projection	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 g7239.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g7239.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples

39TPM > 0

1Conditions

192.8Max TPM

33.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	33.05	192.80

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	192.80
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	188.47
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	56.57
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	53.34
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	44.86
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	42.91
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	38.32
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	29.53
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	28.68
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	27.89
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	27.65
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	27.22
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	26.74
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	25.33
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	24.55
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	23.59
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	23.44
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	23.39
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	23.07
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	22.19
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	21.94
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	21.27
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	20.98
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	20.66
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	20.54
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	20.03
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	19.92
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	19.02
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	18.76
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	17.59
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	17.27
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	16.29
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	15.82
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	15.51
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	15.20
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	14.96
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	14.74
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	14.37
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	13.69

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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 Acropora digitifera 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	34	g6549.t1	0.970835054616565
Negatively correlated	4	g20572.t1	-0.723555661816662

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 Acropora digitifera, 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.

Peak calls overlapping this gene

Assay	Sample	Peaks	Region

No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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 →