Gene detail

Detailed information of CAB4007138.1 in Paramuricea clavata

Genomic Location: pcla8_s005831:12622...16902
NR annotation: CAB4007138.1, translin-associated X isoform X2 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A077466

CCTCGTCCAACAGTAACTTTCCCTTCAGATACATCAATTTTGTAATCTTTTTCTATAGATACTAGTGCAAAACTGCTCATTTTTAGGGTTTTGTCTCTCAATTTAGCAATAAAACTTCGAACATTTTATGTTTTGATGTGAAGTATAATCTGAGCCCACGAGCATAATtgtgtaatataaatataagACAGACTTAGATCAGCGGTATATCGTATCAGTATAAAACAGTCTAGCGCAATCATGGAAACTGCAACTTTTGGTCGAAAAAGACGAAGGAAAAACGAAGATAGTTCAGCAATGTCAGACGAAACGTCTGCCAAAAAGCCTCTTAAAGATGCTTCACCTATTCTTCAACTATTTCAAGGTTTCCAAACGGAGCTAGACAGCCGTCATGATAAATATGAACGGATAGTGAAATGCAGTAGAGACATAACCACACAAAGTAAACGGGTTATATTTCTACTACACCGCGGCTTGGACGAGAAATCACGAGCGAAAATATTAGAAGAAGCAGCAGGAAAGTTTGTTGCAATTAAAGAATTGTTTAAAAAGATAGCCGCAGAGCTCTTATATGAGGATTGTTATCAATTCGTAAGAGCTTATTCGCCTGGTCTGCAAGAGTTTGTCGAGGCATATTCGTTTTGGTATTTCTTAAAACATGGAACTTTAGTTTCATTTGAACAGATCTGTAGGGAACTTGTGTTTGGGAATGCATCAGAAAGTACCAAAATAGAGCAAGTTAAACCACATGTCCACAACCCCCCTGATGAGAACATTCAGGTCCACAACCCCCCTGATGAAAACATTCAGGTCTACAACCCCCCTGATGAAAACATTCAGATCCCAAACCCCCCTACAGAGAACACCCATGTCCCTAACCCCCCTGCTAATATCCAGGTCCCCATCCCCCCTGCTGAGTACATCCTAGGTATATCAGATCTCACTGGTGAACTAATGAGGCTAGCTATAAACAGCGTTGGACAAGGAAATCTCACAACCCCCctggaaatttgcaaaattttgcGTAAAATCCACGACGAGTTCATCATGTTTGGAAATCAGCAGCGAGGTTTTCCTAAGAAACTGGAGGTCTTGAAAAACAGTTTAAAGAAAGTAGAAAACACTTGCTATACAATTCATATCCGAGGCTCAGAAGTCCCGAAGAATATGTTAGCAACACTGATAGCTTCAAATACAGACCCTACTGTAGATGGACAATAAACTGCATGTTTTAGGTGATAAATCATCAACATATAGTGACTCATGTACATATTGCagtacaaataaaatacaactTGTTTGAAATGCAACAAACTTGGTTTTCACCCACTAtgcatattttaattaacataaGTACATAACTACATTTTATACAACGTTTTCCTAATTTAACCCCCCTAATGTTTGTCTATACAGTCCTTCagttttaattaaatgtttttaactaCAATGTTTTTAACTACAATATAATACAGACTGGAGTACTTCTATAATTTATAACTACACACTATACAAAGTCAAATTTAATCTTGTCAGTTTCTCAACCTGCCTGAGTAACTACTTCCcaaatttgcttgagtgcataTGAGATAATTGTACAAGGTCAAGGTCAAGCAAACTTGGGAAGTGATTATACTCATGCAGTGTGCTAATGAAACTGACCACAAACTTTCTCAAATACCTATTCTAAATTACAcaatacattttttattaatattaacataaattaatatGTTGGGGGTAATAATTAACTCTTAGGTAACATGAGTGCAAGCTTTTTCATATTTGTCTTATcaacaaatctttcaaaatttaTGTCCTTACACTCCAGATCATTCACATTGTTACAGAAGAGTTAAATAAAACCAACAAATCATTTAAAAATGCTTCATTTTTATGTAGAAGCAGAATATGTATTTCTACTTACAGCTTTGCATGCTACAcccaaaatatattttcatccCACTTTATGAAAGCTGACTTAGTACTTCGCTTATATAAAGTAATGTCATTATTCAGCTTCGAAAACCTGGCCTTAATTAAAACCCAAGTAATATTCTAGCAGTAACTCAACACAAGTCCATTTGGTTTCTTAAACCTTCAAATCTATCTAATGCATACTACATTCCTACAAAGTTAGATGCttagataaaaaaattaattcctaactatatcaattttataataattgcaATTACTTGTATTAAATGAAACTCCAGGCATTTTAAAATAAGAATAAGCCATTTCTGCAACAATGAAAGCTATAGAGATGCCAGATTCCTCTTACAGtcatattttactatttctttATATTCTCTTACTTCAAACCCAAGACTTGGATGAAGTGTTACAGTACTTCCTCAGACAGTCAACTAGTTGCACTCACACTAGGAAGGCTTCGGAATAACCCTTGTGGCAACATGAGCTTGCAACATTGCAAGAATTTCTTTGGCTCTGGCATGTGCGAGATGACATCCCACTTGTTTGTCGTACAATCATAACATTCCACGCTGTTATGGTATCTCGTACCTGTACCCTCACCACCAAACACGTACACCTTCTCACCATGAACAGTTATACCTGCAAAGGCTCGTGGGACACTAAGATCGGCAACAGGGAACCAGACGCCTGCCGTGGAGTTGTACATCTCGCAACTTCGCAGGTACGTCCGAATGACAACCACATGATCAATGGTGTCAACTTCACCAACTTCGTTGATACCGCCAACCACAAGGATGTTGCCACTACCAACCGATGCCGCGACGGCGTAAGCTCTCTTGTGAGACATCTCACTCATTCTTTCCCAAGTGTCGGCTGTGATGGAATAACGCTCCATCGAGGACAGCATCTGGTTGTCACTTGCCTTTCCACCAATCGCGTACAGGAAATCACCAACGGTGACCAGACTTGCACCACTTCGCGAAACATGCAAAGGCGTTTTCACTTCCCATCTTTGGGTCGCAGGGTCGTACCGTTTCAGGATACCAAGGCGGATACCATTCTCAACAATTCCTCCAGCGACGTAAAGCGAGTTACCAACTGCAGCAACAGCCATTCCCTTCATCGGAGTGGGTAAAGGTTGGCTAGTGGACCATTTCCTTGCTTTCACATCAAACTTCTCAACCTCGGCTGTGAATCCATTCTTGGAATACCCGCCAAGGACAAAGACATCATCTCCAATTGTGGCCACGCCATGGCTGTACCGAACCGTGCTCATTGATGGAATCTTGAACCAGGCATTCTGAGAAGGAACGAAGAGATATGAGGAAGCAGTCGCTCCTGACGGTTCTCGTCCACCGTTCACAAACACACAATCGTAAAACCGAGATGGAATCACCTTCGTGGCATCTTCGGTAACATAGCACTCCAGTATCATCCGCATTAATAGATCTGAACAAATCGGATCATCGGTAACTAGCTTTTCGTTGGCAATCGTCTCGGCAAGGTAGGTCCTACTAACATCTTGAAGCCGAACCTTGCCAAAGAGCTTAGGGAAAAATCCTACTCGATTTGTTAAATCATGTTTCACCCATCTTAAGATGCCTTCATAAAGTTCCTCTTCCGCGAACAAAACTAACTCGTCACTTGAAACTATTTCTAATAATTGCTCAGGGTCAGTTAATAAATAATCCTCAGTTTGAGATATTGCAGTAAaattttcaactaaaaaatCCCGAGTCAGTTCACGCAAGGGTTCGCAATGATATCGCCCAGCAAAGCCATGTAATGCAATCCCGTTCGATAAGTttacattttgttgcaaaaatcTACACCCCAGCTCCTTCAGTTCTGTGACATTGAAATAATCCGCGGCGACGATCAAAGCTTCAACGTTTTCCTGTGTCAATTGTACTTTAGTTGTGTACAAAAAGGTGAGAAAATCATCCATACGATGCACTAAATCGACGGGACATTTTAGATCGATAACACTTTGCTTTCTTTCTTTCATGTTGGCAGTGAACAGCGTTCGAAAATACGGACAGCTCGATGACAAGACTACTTTATGGACATCGAATTCTTTTCCTTCTAATCGCAATTTCGCGTCGCAAAGTGTTTCATCTTGGCGAAATTCATTCAGCTGATGCAGCATTTTCGTACCTAACCTTTCGCTAGTCGAGACAACGCTTTCCAGATATTCATCCTGTTCTAAACTTTCCATTGAGTGTGAAGATCTTACTTCACTATCAATTGAGCCATCGAAATCAACCATCGCTCGCTCGTGCCTTGTACAAATACGGGAGAAGTGACGCGAATGATATTCAAcaccaaaataattttttg

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9QZE7	Translin-associated protein X OS=Mus musculus OX=10090 GN=Tsnax PE=1 SV=1
Q9JHB5	Translin-associated protein X OS=Rattus norvegicus OX=10116 GN=Tsnax PE=1 SV=1
Q99598	Translin-associated protein X OS=Homo sapiens OX=9606 GN=TSNAX PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007910 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01997 all species →	Translin	Translin family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002848 all species →	Family	Translin family	Interproscan
IPR036081 all species →	Homologous_superfamily	Translin superfamily	Interproscan
IPR016069 all species →	Homologous_superfamily	Translin, C-terminal	Interproscan
IPR016068 all species →	Homologous_superfamily	Translin, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10741 all species →	TRANSLIN AND TRANSLIN ASSOCIATED PROTEIN X	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004521 all species →	Molecular Function	RNA endonuclease activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0043565 all species →	Molecular Function	sequence-specific DNA binding	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 CAB4007138.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4007138.1 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

18TPM > 0

4Conditions

119.3Max TPM

14.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	13.29	19.41
apical branchlet · Temperature treatment at T0	6	5	6.14	14.56
apical branchlet · Temperature treatment at T25	5	4	31.68	119.30
apical branchlet · Control at T0	4	3	4.79	9.49

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
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	19.41
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	18.26
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	16.25
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	14.66
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	7.59
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.59
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	14.56
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	11.73
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	5.34
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.04
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.17
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	119.30
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	16.57
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	14.45
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	8.10
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	9.49
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	7.18
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	2.50
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	7	CAB4033523.1	0.975749374941865
Negatively correlated	3	CAB3991442.1	-0.494849295270731

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 →