Gene detail

Detailed information of asel_s0049.g4.t1 in Acropora selago

Genomic Location: sc0000049_pilon:71968...85645
NR annotation: XP_015756245.1, PREDICTED: RNA polymerase II subunit A C-terminal domain phosphatase SSU72-like [Acropora digitifera]
Species Acropora selago · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6NRQ7	RNA polymerase II subunit A C-terminal domain phosphatase SSU72 OS=Xenopus laevis OX=8355 GN=ssu72 PE=2 SV=1
Q5ZJQ7	RNA polymerase II subunit A C-terminal domain phosphatase SSU72 OS=Gallus gallus OX=9031 GN=SSU72 PE=2 SV=1
Q9NP77	RNA polymerase II subunit A C-terminal domain phosphatase SSU72 OS=Homo sapiens OX=9606 GN=SSU72 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006320 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04722 all species →	Ssu72	Ssu72-like protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006811 all species →	Family	RNA polymerase II subunit A	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR20383 all species →	RNA POLYMERASE II SUBUNIT A C-TERMINAL DOMAIN PHOSPHATASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004721 all species →	Molecular Function	phosphoprotein phosphatase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005847 all species →	Cellular Component	mRNA cleavage and polyadenylation specificity factor complex	Interproscan
GO:0006369 all species →	Biological Process	termination of RNA polymerase II transcription	Interproscan
GO:0006378 all species →	Biological Process	obsolete mRNA polyadenylation	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:0008420 all species →	Molecular Function	RNA polymerase II CTD heptapeptide repeat phosphatase activity	Interproscan
GO:0070940 all species →	Biological Process	obsolete dephosphorylation of RNA polymerase II C-terminal domain	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
K15544	SSU72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72	EC:3.1.3.16	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of asel_s0049.g4.t1 across 24 RNA-seq samples of Acropora selago. 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.

24Samples

24TPM > 0

1Conditions

102.9Max TPM

68.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
coral larvae	24	24	68.61	102.91

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR14308027	coral larvae	coral larvae	not recorded	not recorded	SRP315987	102.91
SRR14308004	coral larvae	coral larvae	not recorded	not recorded	SRP315987	101.72
SRR14308013	coral larvae	coral larvae	not recorded	not recorded	SRP315987	94.27
SRR14308026	coral larvae	coral larvae	not recorded	not recorded	SRP315987	84.86
SRR14308010	coral larvae	coral larvae	not recorded	not recorded	SRP315987	76.60
SRR14308007	coral larvae	coral larvae	not recorded	not recorded	SRP315987	73.20
SRR14308016	coral larvae	coral larvae	not recorded	not recorded	SRP315987	72.37
SRR14308006	coral larvae	coral larvae	not recorded	not recorded	SRP315987	71.24
SRR14308008	coral larvae	coral larvae	not recorded	not recorded	SRP315987	69.31
SRR14308023	coral larvae	coral larvae	not recorded	not recorded	SRP315987	67.42
SRR14308024	coral larvae	coral larvae	not recorded	not recorded	SRP315987	66.27
SRR14308022	coral larvae	coral larvae	not recorded	not recorded	SRP315987	65.47
SRR14308017	coral larvae	coral larvae	not recorded	not recorded	SRP315987	65.27
SRR14308020	coral larvae	coral larvae	not recorded	not recorded	SRP315987	65.11
SRR14308012	coral larvae	coral larvae	not recorded	not recorded	SRP315987	64.11
SRR14308015	coral larvae	coral larvae	not recorded	not recorded	SRP315987	63.55
SRR14308019	coral larvae	coral larvae	not recorded	not recorded	SRP315987	63.48
SRR14308021	coral larvae	coral larvae	not recorded	not recorded	SRP315987	62.85
SRR14308005	coral larvae	coral larvae	not recorded	not recorded	SRP315987	62.56
SRR14308011	coral larvae	coral larvae	not recorded	not recorded	SRP315987	61.15
SRR14308025	coral larvae	coral larvae	not recorded	not recorded	SRP315987	56.15
SRR14308014	coral larvae	coral larvae	not recorded	not recorded	SRP315987	55.03
SRR14308009	coral larvae	coral larvae	not recorded	not recorded	SRP315987	42.95
SRR14308018	coral larvae	coral larvae	not recorded	not recorded	SRP315987	38.83

Source: CnidoSite RNA-seq expression matrices (ASELA_TPM, StringTie quantification over 24 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 selago 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	12	asel_s3416.g1.t1	0.86449252296197
Negatively correlated	5	asel_s0111.g16.t1	-0.751089062654426

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 selago, 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.

DNA methylation (bisulphite samples)

Sample	Methylation profile
Coral_Fragment_Parent	open
Larval_Pool_Offspring	open

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.

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 →