Gene detail

Detailed information of CAB3979603.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3979603.1, regulator of nonsense transcripts 1-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3979603.1 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
F1RCY6	Regulator of nonsense transcripts 1 OS=Danio rerio OX=7955 GN=upf1 PE=2 SV=1
Q92900	Regulator of nonsense transcripts 1 OS=Homo sapiens OX=9606 GN=UPF1 PE=1 SV=2
Q9EPU0	Regulator of nonsense transcripts 1 OS=Mus musculus OX=10090 GN=Upf1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004555 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13087 all species →	AAA_12	AAA domain	Domain	Interproscan
PF13086 all species →	AAA_11	AAA domain	Domain	Interproscan
PF18141 all species →	UPF1_1B_dom	RNA helicase UPF1, 1B domain	Domain	Interproscan
PF04851 all species →	ResIII	Type III restriction enzyme, res subunit	Family	Interproscan
PF09416 all species →	UPF1_Zn_bind	RNA helicase (UPF2 interacting domain)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR018999 all species →	Domain	RNA helicase UPF1, Cys/His rich zinc-binding domain	Interproscan
IPR045055 all species →	Family	DNA2/NAM7-like helicase	Interproscan
IPR040812 all species →	Domain	RNA helicase UPF1, 1B domain	Interproscan
IPR041679 all species →	Domain	DNA2/NAM7 helicase-like, C-terminal	Interproscan
IPR041677 all species →	Domain	DNA2/NAM7 helicase, helicase domain	Interproscan
IPR047187 all species →	Domain	Upf1-like, C-terminal helicase domain	Interproscan
IPR006935 all species →	Domain	Helicase/UvrB, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10887 all species →	DNA2/NAM7 HELICASE FAMILY	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0004386 all species →	Molecular Function	helicase activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase 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
K14326	UPF1, RENT1; regulator of nonsense transcripts 1	EC:5.6.2.5 EC:5.6.2.3	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3979603.1 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

16TPM > 0

4Conditions

56.4Max TPM

20.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	35.31	56.41
apical branchlet · Temperature treatment at T0	6	4	18.39	42.12
apical branchlet · Temperature treatment at T25	5	4	11.29	20.79
apical branchlet · Control at T0	4	3	14.23	33.39

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	56.41
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	49.18
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	45.25
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	34.01
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	27.00
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	42.12
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	26.34
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	25.70
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	16.18
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
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	20.79
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	19.84
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	12.71
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	3.09
SRR19977434	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	33.39
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	12.73
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	10.80
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.