Gene detail

Detailed information of g3220.t1 in Acropora digitifera

Genomic Location: chr2Alt:10168201...10173902
NR annotation: XP_015755571.1, PREDICTED: uncharacterized protein LOC107335116 [Acropora digitifera]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Pfam domain

No Pfam domain signature was recorded for g3220.t1 in Acropora digitifera.

InterPro

No InterPro signature was recorded for g3220.t1 in Acropora digitifera.

PANTHER

PANTHER term	Description	Source
PTHR34716 all species →	BTB DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

No Gene Ontology signature was recorded for g3220.t1 in Acropora digitifera.

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
K22453	TFF2; trefoil factor 2	-	Structural proteins	-	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g3220.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

1,334.2Max TPM

442.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	442.75	1,334.19

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
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	1,334.19
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	944.30
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	878.95
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	784.31
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	741.81
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	727.62
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	702.71
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	628.45
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	626.26
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	532.86
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	520.00
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	456.25
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	433.31
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	433.20
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	398.55
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	395.37
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	392.30
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	391.74
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	384.58
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	378.41
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	352.01
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	351.53
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	350.01
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	347.66
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	339.97
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	325.76
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	321.59
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	306.51
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	292.47
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	278.17
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	259.29
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	254.35
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	234.66
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	224.39
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	209.00
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	191.11
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	189.52
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	180.67
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	173.28

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	15	g23569.t1	0.813256367471949
Negatively correlated	17	g16821.t1	-0.67165232721765

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 →