Gene detail

Detailed information of CAB4032239.1 in Paramuricea clavata

Genomic Location: pcla8_s019835:4247...6495
NR annotation: CAB4032239.1, ectodysplasin-A-like isoform X2, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A047645

GTGTAATGAATCAGCTCATATTGTTGGGACAGGAGGTAACATTCAATCAGCTCCACCTGCACCCAGAGGTAAATTTATATGAGGCGGCGAGTCTTTGGATGTTAGTTTGAGGTGGTCGGCCTTTGGATGTCCGCTTGAGGTGGTGGTTTTTTATGTTAGTTTCAGTTGGTGGATCTTTAAGTTGCACTTCCATGTCAGAGGCGTGGCGGGCGGGGACTGGGGGTCCCGCCCCCTCAGAAAATTCATTCTATAAAAATAAGTGAAACCTGGCCCACCTTGATTTTTGCTGACCCTCTCTTACCCCTGACACCCAACTCCTGTTTTACCTTCACGTTTAAGGTGCTTAACTTCAAGTAAATAAATCCTTATTTTCGTAATTTAAATTAAGAATAGACGATGGTTATTGAATCACACAGATTAACGGTTTGATTAATGATTTTCAGTTAAAATTCATAACTGTTTGGCAGTATACTCCAAATATGACTAGCCTGAGTCATGCACTTCTTAGTGGCTGGAAGATTAGTCAAGTTCGCCCTTTCAAATTTCGGCTCTATACTGTCTTGCTATACGCAGGCTGCACTGATTCTATCGTTTCAATTGTGTCAATTAATCCACGTCTCTGTTGGATTTCGTTGCAAAATTCTGTAAATCAGGTGTTAAGGCCTTGTCACACTATTGCGCATAAGAGAAACGTGcaatgagaagcgtatgaaaattaatgaaatgatTTTTATACGCACAAAAaacctttgaaatgccagcgtatgagtaccgtacatctggcgtacctctagcgtgtgcctagagtatgcttgcacattcagcgtgtgcctatagagtatgcttatcgtatgaAACGATACGATGAagtaagtttaaaaataaacgttgtctaagccgagaaaatcaaagctaaagtttatgtaaataaacatgattttttatcacatataaaaccacggacacggcagtgatttcttttgtatctcctcatgaattattaattaattatgctGCTATTCAATTAAATCCTCAAATTTGATGACAGTTCATAAGCTCTAATTTAGAAGCACAAAAATCACTATATGCACTTATAGAAACTGTAAGAACAATACTCACTATTCTTGAGTTGAGATATACCAACTGCAGTTTTGAACGAGGTGTATAATCACGCGTATTATTTAAAGTTGGTaaggtattaatatttgtaatGAGGCACTGATCATTAATACTTCGTTGTTTAATCTCAAGAAATACTTGAACTTTTTCCTGATGAACTTTCTATTTCCTTTTAGATGTTTATACAGTAACATCCTGGAGAAAACAACACCGATCTGGAAAAATGAAGTACGAAGACAACGGTCATTTAAGAATCAATGTTGATGGAGTTTACTTTGTTTACAGTCAAATGTATTACTTTGATCAGAATAACACTTATACTGGTTTCAATGTGTATATCGACAACAAGAGAATCCTGAAAGCAATCTACAGTATTGTTGATTATCATAAACCATATCATACTCAGTTTATCAGTGGTGTTTTCAAAATCTACAAGGGCCAGACAATATGGGTAGGAATGAAAATTaagaggaaatattttttcgacGAAAGTTCAGCTTTCTTTGGTGCATTTATGTTGCATCCTTAAATTAATACGATCATTTTGGCAAAGCATGAAAAATCGACAAATAATCCTCTAAAGGTAGCATATGCAAAAATTACTTACCAATATCGcgattttatcaatttatcccAATGGATTGAGTTAAAATCACGATACAGACCGTGCCATCGGTTTCTGCTATGCCTATATATGATCATCCCTCTCGTCTTCTTTATTATGGTAGATTATGATGGGGTCCATGCAATCATTCATGCAATTTATAAAGTAATTAGTTAGAATTTTTGATTACAACAATATCAATAGACATTATGCATTCTTTTTCTAACGACTAGTAGTATAacataaaattgtaaataattattgtataagCAGTATCAACTATCAAGTATCATATATACACAAATAAGGCAAGAAATGTACCGAGTACTTTTAATAGTAATTTTTAAGTAATTTTGTTAATTGAAATGTAAATATCAACTTCTATTTCTTAGACTCGTTTGTAGATACtataaactaataataaaacTGTATAACCGACACTGAAATAATTAGAAAATATTGGACTGGCCCAGTTGGATCATAATCATACATTAGTTAAAGTTAACGacgttttatacaaccggcc

Protein

UniProt (Swiss-Prot top hit)

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

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000886 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00229 all species →	TNF	TNF(Tumour Necrosis Factor) family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR021184 all species →	Conserved_site	Tumour necrosis factor, conserved site	Interproscan
IPR006052 all species →	Domain	Tumour necrosis factor domain	Interproscan
IPR008983 all species →	Homologous_superfamily	Tumour necrosis factor-like domain superfamily	Interproscan
IPR051748 all species →	Family	Tumor Necrosis Factor Ligand Superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15151 all species →	PROTEIN EIGER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005164 all species →	Molecular Function	tumor necrosis factor receptor binding	Interproscan
GO:0006955 all species →	Biological Process	immune response	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005615 all species →	Cellular Component	extracellular space	Interproscan
GO:0048018 all species →	Molecular Function	receptor ligand activity	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

No KEGG orthology assignment for CAB4032239.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4032239.1 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

7TPM > 0

4Conditions

13.8Max TPM

2.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	3	4.23	13.84
apical branchlet · Temperature treatment at T0	6	2	1.53	5.85
apical branchlet · Temperature treatment at T25	5	1	0.45	2.23
apical branchlet · Control at T0	4	1	1.46	5.86

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
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.84
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	7.89
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.64
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	5.85
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.34
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.23
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
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
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	5.86
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977446	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	31	CAB3997129.1	0.996492181660734
Negatively correlated	4	CAB4017758.1	-0.628821063407998

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 →