Detailed information of XP_029200475.2 in Acropora millepora

Genomic Location: NC_058067.1:16509954...16514417
NR annotation: XP_029200457.2, zinc finger protein 271-like [Acropora millepora]
Species Acropora millepora · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
No Swiss-Prot hit above the reporting threshold for this gene.
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0010953 (this species only) · gene tree & orthology
Transcription factor familyzf-C2H2 · all TF in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13912
all species →		zf-C2H2_6C2H2-type zinc fingerDomainInterproscan
PF00096
all species →		zf-C2H2Zinc finger, C2H2 typeDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036236
all species →		Homologous_superfamilyZinc finger C2H2 superfamilyInterproscan
IPR013087
all species →		DomainZinc finger C2H2-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR24376
all species →		ZINC FINGER PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000978
all species →		Molecular FunctionRNA polymerase II cis-regulatory region sequence-specific DNA bindingInterproscan
GO:0001228
all species →		Molecular FunctionDNA-binding transcription activator activity, RNA polymerase II-specificInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K09228KRAB; KRAB domain-containing zinc finger protein-Transcription factorsko03000deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_029200475.2 across 54 RNA-seq samples of Acropora millepora. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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.

54Samples
0TPM > 0
2Conditions
0.0Max TPM
0.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole larvae 30 0 0.00 0.00
branch 24 0 0.00 0.00

Per sample · hover a bar for the full sample record

Show the sample table (54 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR1929605 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929606 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929607 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929608 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929609 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929610 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929611 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929612 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929613 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929614 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929615 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929616 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929617 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929618 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929619 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929620 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929621 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929622 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929623 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929624 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929625 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929626 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929627 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929628 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929629 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929630 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929631 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929632 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929633 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929634 whole larvae whole larvae adult not recorded SRP056536 0.00
SRR1929581 branch branch adult not recorded SRP056536 0.00
SRR1929582 branch branch adult not recorded SRP056536 0.00
SRR1929583 branch branch adult not recorded SRP056536 0.00
SRR1929584 branch branch adult not recorded SRP056536 0.00
SRR1929585 branch branch adult not recorded SRP056536 0.00
SRR1929586 branch branch adult not recorded SRP056536 0.00
SRR1929587 branch branch adult not recorded SRP056536 0.00
SRR1929588 branch branch adult not recorded SRP056536 0.00
SRR1929589 branch branch adult not recorded SRP056536 0.00
SRR1929590 branch branch adult not recorded SRP056536 0.00
SRR1929591 branch branch adult not recorded SRP056536 0.00
SRR1929592 branch branch adult not recorded SRP056536 0.00
SRR1929593 branch branch adult not recorded SRP056536 0.00
SRR1929594 branch branch adult not recorded SRP056536 0.00
SRR1929595 branch branch adult not recorded SRP056536 0.00
SRR1929596 branch branch adult not recorded SRP056536 0.00
SRR1929597 branch branch adult not recorded SRP056536 0.00
SRR1929598 branch branch adult not recorded SRP056536 0.00
SRR1929599 branch branch adult not recorded SRP056536 0.00
SRR1929600 branch branch adult not recorded SRP056536 0.00
SRR1929601 branch branch adult not recorded SRP056536 0.00
SRR1929602 branch branch adult not recorded SRP056536 0.00
SRR1929603 branch branch adult not recorded SRP056536 0.00
SRR1929604 branch branch adult not recorded SRP056536 0.00

Source: CnidoSite RNA-seq expression matrices (AMILL_TPM, StringTie quantification over 54 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 millepora 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated0not in this network-
Negatively correlated0not in this network-

This gene has no edge at all in the Acropora millepora network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.

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 millepora, 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.

DatasetTissue / stageCellsCell typesThis geneMarker of
AMILL_whole_adultWhole adults · Adult tissues/organs25,16427not 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.

DNA methylation (bisulphite samples)

SampleMethylation profile
planulaopen

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw 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 / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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