Gene detail

Detailed information of CAB4018220.1 in Paramuricea clavata

Genomic Location: pcla8_s010265:16192...17448
NR annotation: CAB4018220.1, selenocysteine-specific elongation factor [Paramuricea clavata]
Species Paramuricea clavata · 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
Q9JHW4	Selenocysteine-specific elongation factor OS=Mus musculus OX=10090 GN=Eefsec PE=1 SV=2
P57772	Selenocysteine-specific elongation factor OS=Homo sapiens OX=9606 GN=EEFSEC PE=1 SV=4
B5ZC31	Elongation factor Tu OS=Ureaplasma urealyticum serovar 10 (strain ATCC 33699 / Western) OX=565575 GN=tuf PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007862 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03144 all species →	GTP_EFTU_D2	Elongation factor Tu domain 2	Domain	Interproscan
PF21208 all species →	euk_SelB_III	Selenocysteine-specific elongation factor, eukaryotes, 3rd domain	Domain	Interproscan
PF21131 all species →	eEFSec_4th	eEFSec C-terminal RIFT domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004161 all species →	Domain	Translation elongation factor EFTu-like, domain 2	Interproscan
IPR050055 all species →	Family	Elongation factor Tu GTPase	Interproscan
IPR049393 all species →	Domain	Selenocysteine-specific elongation factor, 3rd domain	Interproscan
IPR049394 all species →	Domain	Selenocysteine-specific elongation factor, C-terminal RIFT domain	Interproscan
IPR009000 all species →	Homologous_superfamily	Translation protein, beta-barrel domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43721 all species →	ELONGATION FACTOR TU-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0001514 all species →	Biological Process	selenocysteine incorporation	Interproscan
GO:0003746 all species →	Molecular Function	translation elongation factor activity	Interproscan
GO:0006414 all species →	Biological Process	translational elongation	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 CAB4018220.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4018220.1 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

9TPM > 0

4Conditions

12.3Max TPM

1.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	3.55	12.28
apical branchlet · Temperature treatment at T0	6	3	1.92	9.03
apical branchlet · Temperature treatment at T25	5	1	0.31	1.53
apical branchlet · Control at T0	4	1	0.46	1.85

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	12.28
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	5.27
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.23
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.51
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	9.03
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.58
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.93
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	1.53
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	1.85
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.