Gene detail

Detailed information of CAB4043199.1 in Paramuricea clavata

Genomic Location: pcla8_s040226:197...2812
NR annotation: CAB4043199.1, eukaryotic translation initiation factor 5A-1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A031712

CTAACTGCATCAACAAACTTTTCTTTTGTTCACCCTAGGTTCATATGGTTGGCCTCGACATCTTCACTGGCCGCAAGTATGAAGATATCTGTCCATCCACGCATAACATGAATGTGCCAAATGTCAGCCGCAAAGATTTTCAGTTGGTTAATATTGAAGAGGGCTTTACACATTTGATGGACGACGGTGGAGATGTGAGAGAAGACATGAAAGTACCAGAAGGGGATTTGGGTAAGGAAATCCAGACAAAATTCGATAATGGAGATGAGTTTATGTGTACAGTTCTTAAGGCTGTCGGCGAGGAACAGATTATTGCTGTAAAATCTTCAGCTAAGAAGGATTAACTGTAACATTTTGTGGTATGAACTACCTCATCGATGAGGAATTAAAAACCTATTTAGACGTTTGACAGTTTGAGTTTTATTTTATGTATCTAGGCTGGTTGGTTTACCTTACACTACCTTCTCTTTTTTCAAGACAATATATTCCTTTCTATTGTAAGACAATATCTTTTTGTAGACTGGTTTGTCAAAATGTCTGCAAAATGTCAGCGTTGTCTGTTTGTAATCTGACATTTGATTTGAATTTGAGATAAATTCTCAAACCTATCACAACTTTAAGGGGTGCACCTGAACCAATATTTTAAGTTCTGGCCTGAACTGTGTTTATTTAATCATGTAAGTTTCTTTGTCAGATGTCAAGCTGGCATGCAAAATCGTGAAGTACATACTGTACcttaaaaatgttgaaaattgaaatatatgTCTATGGTGGCATGTGTAATTAAAATGATGTCAATATTGAGATCTGTTAAACTATTTAGTTGAAATTCATCAATTatcaataataatatttttaatgaaaacagAGTTTTCATCAGAACTGACTGGAACCAAGTTTTGGTTCCATATTAATTTTGTTGTCTTGGATATCGTCATGACAACATATATTACCAAATATTGTTTATTCATTGTCATTGAGAAATATTTTAGTTTGGAAATCTTTTCTGACTGGCACATGCGCAGACATTTTTGCAAACAGTTCAGTGGGTGTCGTAATTTAGTGGATTCGGTCTCTTTGAAAATTGACAGTACTATAGTCTATAGCGAATTGAGACAATTGTTTTGCAATAGTTTGCAAATGAAGTTCTAATCTTACAGCAAAAATGCAATTCTAAATCAAATAAAGTGTTTTTTGAAGTGATATTTTAATCCTTACTGAGTACAGTAGCTTTGATTTTTCCTATCACTGGAACAATAATACTAAGTTACTGTACCTTGTTCTATTCTACAGTATGCTCCATAAACCAGAAAAATAGTAACTAAGCTCGTCAGTTATCTGAATGCTTAGTTGCTTTTGTTCTATTCCATGCTTTCCTAAACTACTGTATAACACTTCACAATACTAACTAGTCGTGTGaactttgttctattctatgatTTCTTGAACTGGGACAGTAGCAActtgttttcatattttatactttttgtaaactatttaaaaaatagtaattaatTTAGTAACTAGGCAGGTCGATTATCCACAGTTGTGAATTTACATTGTACAAACGGTAACTAATTTTTctattccagatatatatatcgTACTACATATCTTAGGAAAGCGTAGCAATCTATTTTTTCAATCACTTCATGACAAAATTAAGCCTTAGAAAATTAAACCGGTTTGGATACGGAGGTTCAATACCATTACTAAAATACGATACTATGGAGCAGATCGTTTGTTATCACTATTTGCAAGCAAGCAACTGCGCAGCAAGGtattagttttaatatactgttGTTTCCCAAGGAAGAGCGTCATCTTGAAGGCCACAAGGTCGACTAAACTCTTGACCGTAAGAATGGATCCATTTGTTGGAAACTAGAAAAAAAAGAAACAGCGTGGTTAGTTGACCGAATTTCTAAACTAATTAGTTGTTTGCAATCAACCTTTTGAGATTTACTTCCATGTTGGAGGAAAACACGCTCCAATACAATAGCTGttaatgagattcttttgttaGCGTTCCTTCAATATGGCCGCCGTGACATCAATTGCATACCAAGAATACAAATTTTAGTCGAATATTAATACGACAACCTAGAAGTTGTTTAAAACGCTGCTGCCAAACTCTGTTGATAATTCATGCTGCTGATATAACTCGCTTTCAGTTTACAAAAGCATAGGAAACTAAGCATTAGAAAACTCACATGGCTAATTATTATTCTAGTTTACAAAGGCATGGAATGGAGCAAATGTACTTAATTATTAGAAAACATACCTGCCTAGGCTAGTTGCTGTTGTTTCAATTTACAAAAGCATACAATAGAACAACTAAGGCCTATATAAACTATgaaaactggccgttgagaaagatcgtaactatttttacgaccatatggaaaccaggctttttaaattaaaacaagcgttaaaacaatttttaatttaatttttttgttaaaacaagCGTCAGTCAGATTTGTGTATCGTACCCCATTTTGATCCAATGATGACAGGGCAAGCAGCATGTCTTGTGGACGAATCCCCTGCCCCCGATTTGCGAAGGTTATACCAGAACACTGCGTCTCCCTGAAACAGAACATGCATGGT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P10160	Eukaryotic translation initiation factor 5A-1 OS=Oryctolagus cuniculus OX=9986 GN=EIF5A PE=1 SV=2
Q6EWQ7	Eukaryotic translation initiation factor 5A-1 OS=Bos taurus OX=9913 GN=EIF5A PE=2 SV=3
P63241	Eukaryotic translation initiation factor 5A-1 OS=Homo sapiens OX=9606 GN=EIF5A PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008228 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01287 all species →	eIF-5a	Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold	Domain	Interproscan
PF21485 all species →	IF5A-like_N	Translation initiation factor 5A-like, N-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008991 all species →	Homologous_superfamily	Translation protein SH3-like domain superfamily	Interproscan
IPR014722 all species →	Homologous_superfamily	Large ribosomal subunit protein uL2, domain 2	Interproscan
IPR020189 all species →	Domain	Translation elongation factor, IF5A C-terminal	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR048670 all species →	Domain	Translation initiation factor 5A-like, N-terminal	Interproscan
IPR001884 all species →	Family	Translation elongation factor IF5A-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11673 all species →	TRANSLATION INITIATION FACTOR 5A FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003746 all species →	Molecular Function	translation elongation factor activity	Interproscan
GO:0043022 all species →	Molecular Function	ribosome binding	Interproscan
GO:0045901 all species →	Biological Process	positive regulation of translational elongation	Interproscan
GO:0045905 all species →	Biological Process	positive regulation of translational termination	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K03263	EIF5A; translation initiation factor 5A	-	Translation factors	ko03012	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4043199.1 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

21TPM > 0

4Conditions

170.8Max TPM

74.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	104.81	170.83
apical branchlet · Temperature treatment at T0	6	6	70.88	100.05
apical branchlet · Temperature treatment at T25	5	5	64.40	109.03
apical branchlet · Control at T0	4	4	45.16	67.62

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	170.83
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	113.01
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	99.01
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	86.75
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	83.35
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	75.92
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	100.05
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	90.28
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	81.95
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	80.45
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	41.43
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	31.08
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	109.03
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	74.11
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	67.35
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	51.38
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	20.13
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	67.62
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	60.29
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	27.04
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	25.71

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.