Gene detail

Detailed information of CAB4003742.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4003742.1, ribosome biogenesis TSR3 homolog [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4003742.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9UJK0	18S rRNA aminocarboxypropyltransferase OS=Homo sapiens OX=9606 GN=TSR3 PE=1 SV=1
Q5HZH2	18S rRNA aminocarboxypropyltransferase OS=Mus musculus OX=10090 GN=Tsr3 PE=1 SV=1
Q12094	18S rRNA aminocarboxypropyltransferase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TSR3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005539 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04034 all species →	Ribo_biogen_C	Ribosome biogenesis protein, C-terminal	Domain	Interproscan
PF04068 all species →	RLI	Possible Fer4-like domain in RNase L inhibitor, RLI	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007177 all species →	Domain	16S/18S rRNA aminocarboxypropyltransferase Tsr3, C-terminal	Interproscan
IPR007209 all species →	Domain	RNase L inhibitor RLI-like, possible metal-binding domain	Interproscan
IPR022968 all species →	Family	16S/18S rRNA aminocarboxypropyltransferase Tsr3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR20426 all species →	RIBOSOME BIOGENESIS PROTEIN TSR3 HOMOLOG	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006364 all species →	Biological Process	rRNA processing	Interproscan
GO:0016740 all species →	Molecular Function	transferase activity	Interproscan
GO:0030490 all species →	Biological Process	maturation of SSU-rRNA	Interproscan
GO:0106388 all species →	Molecular Function	18S rRNA aminocarboxypropyltransferase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K09140	TSR3; rRNA small subunit aminocarboxypropyltransferase	EC:2.5.1.157	Ribosome biogenesis	ko03009	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4003742.1 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

12TPM > 0

4Conditions

19.4Max TPM

5.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	13.96	19.40
apical branchlet · Temperature treatment at T0	6	3	3.90	11.06
apical branchlet · Temperature treatment at T25	5	2	1.89	7.71
apical branchlet · Control at T0	4	1	1.13	4.52

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	19.40
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	19.17
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.85
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.67
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	9.87
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	7.82
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	11.06
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	9.26
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.10
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
SRR19977437	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	7.71
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.72
SRR19977425	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	4.52
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.