Gene detail

Detailed information of g5029.t1 in Acropora digitifera

Genomic Location: chr2Alt:36478865...36488496
NR annotation: XP_027053628.1, retinal dehydrogenase 1-like isoform X1 [Pocillopora damicornis]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

chr2Alt.g5029.t1

GAAGATTCCATAGTGGAGCATATGAGGTAAACCCAATACTTGTGCTAGCTGACTGAGCTGTACAACATCAAAATGCCTGGACCCATAAGAAATCCTGCAATCCAATACACCAAGCTTTTTATTAACAATGAATTTGTGGACTCCGTCAGTGGTAAGACATTTTCCACTTCAAATCCAGTAACAGAGGAAAAAATTTGTGATGTAGCGGAAGGTGACAAGGCTGATGTTAACAAAGCTGTGGAGGCAGCCAAGACAGCATTCAAACTTGGAAGCCCTTGGAGGACCATGGATGCTTCACAACGAGGGCGGCTTCTGTACAAACTAGCAGATCTTGTAGAGAGAGATTCAAATTACTTGGCTTCCCTGGAGACACTAGATTCTGGCAAGTTATTTGTTGATTCTGCAGACGACATGGATATTGTTGTTAAATGTCTGAGGTATTATGCTGGCTGGGCAGATAAGATATCTGGAAAAACAATTGCTGCAGATGGTCCTTACTTTGTGTACACCAGGCATGAGCCAGTGGGTGTGGTAGGCGCCATTACCCCATGGAACTTTCCTCTTGCCCTTCTTGTGCTAAAGGTTGCCCCAGCTGTAGCGTGTGGCAATGTTGTCATTGCAAAACCAGCTGAGCAAACACCACTGACAGCTCTTTATTTGGGCTCATTGATCACAGAGGCTGGGTTTCCCGCTGGTGTTGTTAACATCATTTCAGGCTTCGGCCCCACAGCAGGAGCTGCTATATCTCAGCACATGGAAATAAACAAAGTGTCATTCACTGGATCAACTGAGGTTGCAAGATTGATTCAAGCAGCAGCTGCTGCCTCAAATCTTAAACGTTTAACCCTGGAACTTGGAGGAAAAAGTCCCAATATTGTGCTTGCTGACAGTGACCTGGATTATGCCGTTGAATATTCTCACTCAGCATTGTTCTTCAATCAAGGACAGTGTTGTAGTGCAGGCAGTCGCACTTTTGTGCAGGACACTATTTATGATGAGTTTGTCAAAAAGAGCGTTCAGAGAGCTCAGAAGCGTACTGTTGGGGATCCATTTGATGATTCAGTAGAACAAGGACCACAGATTGATCAGGAGCAATTTGATAAAATCCTCGAGTTGATTGAAAGCGGAAAAAAGGAAGGAGCAAAATTAGAATGTGGAGGTGCTCGACATGGAAGCAAAGGATTTTTCATTCAGCCAACGGTTTTTTCAGGTGTAAAAGATGGTATGAGGATTGCAAAAGAGGAGATATTCGGCCCAGTGCAGCAGATAATCAAGTTTAGTGATATTGATGAGGTCATTGAAAGGGCAAATAACACTGCATATGGCCTGGCTGCAGCAGTGTTCACTAAAGACATTGACAAAGCAACAACCATTTCGCACGGTCTGCAGGCAGGAACAGTCTGGGTTAATTGTTACGAAGCTGGAGCTCCTCAATCACCTTTTGGGGGTTTCAAAATGTCGGGGCAAGGAAGAGAATGGGGAGAATATGGCTTGTTACCCTATCTGGAAGTCAAAACAGTAGTCACAAAAATACCACTGAAGAACTCCTAGGAAAAATAATGGATTGCAAGTGTCAACGTATAATAAATAATAATTCTATTGATCAGCATTTTCTTGGCATAGATGAGAAAGTGAAAAAACGTATAGAGGACAAACTTTATTATTAATATTAATTTTGTGGATTGAAAACTTTCTGAGATTAGTTATTATATTCTATCTTTTATATCGTAAAGTATTATAATAGTAGAATTAATGGTAGTAGGACAAAACAGCACAACCATGAGTTCTTAGTGCCCCATTAGAGAGGATCGACAAGAATCTTGTACCTTGGACAAGTACATCAGTTCTAATTTGGGACAAGTGGGCAAGCATCATGTGTTACAGGACAAAAAAATTCAAAGATTAGGATTGAAACACTGTGCAATAAAAATGTTCAGTGTCTGCTAAGCTAGTAGTGTCTTCTTCAATGTTTTCTCGGCAGTGAATGAGGAGATATTGCTTAAAAAAATTCTGTTTCCTTCCCCCGACTCTGCTGCCGCTGCTGCCGAACCGGAAGTGGACAATTTTTCTATTAAACATGTCATCATACCATCATATTTATATTCTCAAGTGTCTTTTTACTCGCAGAGACGATTAGTTTGAAAACCTGCGAGAGACCACCGTCCTGGCATGGAAAATGTTCCGGTTTCCGCCCGTGGCTCTAAAATCTCACTTTCTTAAGGTCTCTATTCACCGAAATTAGCTGATTTAAAATTATAAAATTAAACACGTCTGTGTTAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P27463	Aldehyde dehydrogenase 1A1 OS=Gallus gallus OX=9031 GN=ALDH1A1 PE=2 SV=1
Q8MI17	Aldehyde dehydrogenase 1A1 OS=Oryctolagus cuniculus OX=9986 GN=ALDH1A1 PE=1 SV=1
P00352	Aldehyde dehydrogenase 1A1 OS=Homo sapiens OX=9606 GN=ALDH1A1 PE=1 SV=2

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00171 all species →	Aldedh	Aldehyde dehydrogenase family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015590 all species →	Domain	Aldehyde dehydrogenase domain	Interproscan
IPR016160 all species →	Conserved_site	Aldehyde dehydrogenase, cysteine active site	Interproscan
IPR029510 all species →	Conserved_site	Aldehyde dehydrogenase, glutamic acid active site	Interproscan
IPR016162 all species →	Homologous_superfamily	Aldehyde dehydrogenase, N-terminal	Interproscan
IPR016163 all species →	Homologous_superfamily	Aldehyde dehydrogenase, C-terminal	Interproscan
IPR016161 all species →	Homologous_superfamily	Aldehyde/histidinol dehydrogenase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11699 all species →	ALDEHYDE DEHYDROGENASE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0004029 all species →	Molecular Function	aldehyde dehydrogenase (NAD+) activity	Interproscan
GO:0016620 all species →	Molecular Function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	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
K07249	ALDH1A; retinal dehydrogenase	EC:1.2.1.36	Retinol metabolism	ko00830	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g5029.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

132.4Max TPM

90.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	90.10	132.42

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
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	132.42
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	129.74
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	122.00
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	119.63
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	119.45
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	119.04
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	118.47
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	114.31
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	113.86
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	113.39
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	109.87
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	107.05
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	106.80
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	106.57
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	104.63
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	104.23
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	103.80
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	101.65
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	101.63
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	101.22
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	97.60
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	96.34
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	96.12
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	94.97
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	93.69
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	90.35
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	89.76
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	89.63
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	87.75
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	86.92
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	85.56
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	84.55
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	27.56
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	26.22
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	24.89
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	24.30
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	23.85
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	22.67
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	21.35

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	35	g24152.t1	0.858018503384859
Negatively correlated	504	g18228.t1	-0.941326147615101

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 →