Detailed information of g30933.t1 in Acropora digitifera

Genomic Location: chr14Alt:25020829...25024120
NR annotation: XP_015758898.1, PREDICTED: DNA-directed RNA polymerase II subunit RPB7 [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)
UniProt accessionDescription
Q5E9B8DNA-directed RNA polymerase II subunit RPB7 OS=Bos taurus OX=9913 GN=POLR2G PE=1 SV=1
P62487DNA-directed RNA polymerase II subunit RPB7 OS=Homo sapiens OX=9606 GN=POLR2G PE=1 SV=1
P62488DNA-directed RNA polymerase II subunit RPB7 OS=Mus musculus OX=10090 GN=Polr2g PE=1 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00575
all species →		S1S1 RNA binding domainDomainInterproscan
PF03876
all species →		SHS2_Rpb7-NSHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR045113
all species →		FamilyRNA polymerase subunit Rpb7-likeInterproscan
IPR036898
all species →		Homologous_superfamilyRNA polymerase Rpb7-like, N-terminal domain superfamilyInterproscan
IPR003029
all species →		DomainS1 domainInterproscan
IPR005576
all species →		DomainRNA polymerase Rpb7-like , N-terminalInterproscan
IPR012340
all species →		Homologous_superfamilyNucleic acid-binding, OB-foldInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12709
all species →		DNA-DIRECTED RNA POLYMERASE II, IIIInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000291
all species →		Biological Processobsolete nuclear-transcribed mRNA catabolic process, exonucleolyticInterproscan
GO:0000932
all species →		Cellular ComponentP-bodyInterproscan
GO:0003697
all species →		Molecular Functionsingle-stranded DNA bindingInterproscan
GO:0003727
all species →		Molecular Functionsingle-stranded RNA bindingInterproscan
GO:0005665
all species →		Cellular ComponentRNA polymerase II, core complexInterproscan
GO:0006352
all species →		Biological ProcessDNA-templated transcription initiationInterproscan
GO:0006367
all species →		Biological Processtranscription initiation at RNA polymerase II promoterInterproscan
GO:0031369
all species →		Molecular Functiontranslation initiation factor bindingInterproscan
GO:0045948
all species →		Biological Processpositive regulation of translational initiationInterproscan
GO:0060213
all species →		Biological Processpositive regulation of nuclear-transcribed mRNA poly(A) tail shorteningInterproscan
GO:0003676
all species →		Molecular Functionnucleic acid bindingInterproscan
GO:0006351
all species →		Biological ProcessDNA-templated transcriptionInterproscan

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
K03015RPB7, POLR2G; DNA-directed RNA polymerase II subunit RPB7-DNA repair and recombination proteinsko03400deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g30933.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
84.4Max TPM
61.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 61.08 84.40

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 84.40
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 77.39
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 72.00
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 70.87
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 70.66
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 70.31
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 69.60
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 67.42
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 66.95
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 66.62
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 65.21
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 65.02
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 64.06
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 64.02
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 62.95
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 62.54
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 62.33
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 61.55
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 61.48
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 60.32
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 59.49
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 59.43
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 59.34
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 59.29
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 59.03
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 58.14
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 57.51
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 57.09
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 56.31
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 55.29
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 55.18
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 54.03
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 53.63
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 53.01
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 52.80
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 50.90
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 49.37
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 46.53
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 40.03

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.

DirectionPartnersMost correlated partnerPCC
Positively correlated1g29882.t10.701842808117369
Negatively correlated31g11695.t1-0.69192664779913

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

AssaySamplePeaksRegion

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.

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.readyopen →
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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