Gene detail

Detailed information of CAB3978534.1 in Paramuricea clavata

Genomic Location: pcla8_s000135:32554...34630
NR annotation: CAB3978534.1, sprouty homolog 2 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A075897-3

CGTAGTTTCACATTGAATATATAAGTTTATGTAGCGTAATAGGTATATGGATATTTAGCAAAACAGACACAGGATACATTGAGTAGACATTTAATCTTCTCTTGTCATTTCAAACGCATTCTAGCATCACGTCATCATGGCGAGAGCAAATAAGCGCTCGTCTTTTAATTGGCAGGTGGGCGGGCATGAAAATTATTCTTAAGGTGTCTGGTTTTAACTTGAGCTTGTAAGCCGTAAGTGATTGCTTGTGGGATTTGAAATAACTCGATTGCCCAAAGTTCCCCGTTATCTTGCACGCCTTTGCCCAAAACACACGAGCGATGATTTTATAAGAAGTGGCGATGGCTTATGAATTAGTCATATTAGCTATCCGATATGTTTATCGCTAAGCATTGCTACACGGCAAAGGCTTGGGGGTCCGGAAGCCAGAAAATTCCAACGTTTCCTGACTGCTCTTATTGGATGTAGCCATTTGCTTTCGGACGGCTTTCCTAGTTTCCTTCGATAGAACAAGTTTTGTTACAAACTATACTGGCTAATTTAGATTTCTCTGCTCCGGGTAAGTTTTGTAAGCGATACTAAGCTCGTTTGTTTGCTTATATCGTCGACCTATTGATCACAGACCGAACCATTTGTATCAAATCAGATCATAGCCGTATGCTATAGGTCACCCTATACGAGTATATAATAAGTACGTCTATATTCTCGCTTGTATTTTTGACCATATAAATAAACCATGAATAACTGTATATTTTTTGTTTACAGAAATTTCACTGTGTTCCGTGGATTGCCGGGTTATTTTGGTTTGTGATTTTACACGTAATTTATGCTGTTCACTTTATATTCATTCTCGACTCTCGATACGTTTGTTGATAAGTAAACCGATGTGGAAGTGTATTTAATGAGACCAGAATGGCATTACATGAAGATGATACATTAATAACTGTTCGTGAAAATCCCTTTGATTCAGACCATTACGATGTTGTGTGGATTAAACGTCGCGACAAGTTTGCAACGACTGATCATCGCTCAAGGCAAAAGCCATCGACTGttgcaaataaattaaaatcgtACGATGGTACAGGTGCTGACGGTAACAAACTCAAGGATAAAACTATAGACTATACATTCATAGACGAGTACTGTAAAGTCTCTGGACCTGTGAAGACACGAGATGAGGATTCCAAACGGAGGGAGCCAAAGACAAATACGACAGCAGCATTTGGTCGACCGAAGGTGCCCTTTGGTAAATTTGTACAACAACATATAGGCGGTACGTCTGACCGTCCGCACACCACAACAGTACAACCCCTAGCCGACATTAGCGAATGTCAACAGGTTCAACGTACATCTTGCAGGAATGCGGAGAATCACGAAACTACGCCATTGAGTGACTGTTACAGCCAAGAGGATATCACTTTAGAATGTTGCGGTCATAATGTTGAAACATTGGTTGATTACTGCACATGTATGTTTTGTGTGAAAGGCTTGCTGTACCACTGTGCTGAGGACTCCTCGTGTTCGGACAATGTTTTAGACAATCCTTGCTCGTGTTCGCCTGTGAACATGGGTTGCGTTGGTCGTTGGAGTATGTTAGGCTTACTTTCAGTATTTCTACCGTGCTTAATGTGTTACCCACTCGCAAGGGGCTGTGTCGGAGTGTGTAAATGTTACAAAGAAGGTGAAAGCCGACGTAAAAGCCGAACTAGAAGTGTACAAAATCGGGAACGCGAGAGACTAACGTGACCCTGAATCTGAAACCGTTTTAAGCGAACGGCGACGAAAATAAATCACGTATTGACTCCGTGTTGATATTGCCCAAATAGTCGGTGGGCCCGAATAACCCAAGAGCGCATAACGAAAATATGGCTCAAATTACTCAAAACCGCAAGGAAATTACGGCGAACGATATTTGTACAGTGTACATATAGAACGAGCGAAATTTAAAATGTGAACCGCAAACTGTCTTCTCACTCATATTTATATACAGCCAAGTTTGTGcttgtaaatattaaatttgtAAAACTCTACATGGCCTGGGGTTTTTTGTGTGGTACTCAGTACCAGAGAGAATGAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9PTL2	Protein sprouty homolog 2 OS=Gallus gallus OX=9031 GN=SPRY2 PE=2 SV=1
Q08E39	Protein sprouty homolog 2 OS=Bos taurus OX=9913 GN=SPRY2 PE=2 SV=1
Q866R9	Protein sprouty homolog 2 OS=Chlorocebus aethiops OX=9534 GN=SPRY2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001233 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05210 all species →	Sprouty	Sprouty protein (Spry)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007875 all species →	Family	Sprouty	Interproscan
IPR051192 all species →	Family	Sprouty domain-containing protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12365 all species →	SPROUTY	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0007275 all species →	Biological Process	multicellular organism development	Interproscan
GO:0009966 all species →	Biological Process	regulation of signal transduction	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0040037 all species →	Biological Process	negative regulation of fibroblast growth factor receptor signaling pathway	Interproscan
GO:0043407 all species →	Biological Process	negative regulation of MAP kinase activity	Interproscan
GO:0046580 all species →	Biological Process	negative regulation of Ras protein signal transduction	Interproscan
GO:0048513 all species →	Biological Process	animal organ development	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
K17383	SPRY2; protein sprouty homolog 2	-	MicroRNAs in cancer	ko05206	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3978534.1 across 21 RNA-seq samples of Paramuricea clavata. 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.

21Samples

16TPM > 0

4Conditions

35.0Max TPM

6.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	10.39	34.96
apical branchlet · Temperature treatment at T0	6	5	5.41	15.24
apical branchlet · Temperature treatment at T25	5	3	3.79	9.12
apical branchlet · Control at T0	4	3	4.77	12.47

Per sample · hover a bar for the full sample record

Show the sample table (21 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	34.96
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	17.12
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.41
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.71
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.16
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	15.24
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.85
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.53
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.69
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.17
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	9.12
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	7.46
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.35
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	12.47
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	5.10
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	1.51
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 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 Paramuricea clavata 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	5	CAB3984150.1	0.879052474980908
Negatively correlated	12	CAB3977473.1	-0.485190658891343

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 Paramuricea clavata, 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.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

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 →