Gene detail

Detailed information of CAB3977020.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3977020.1, 60S ribosome subunit biogenesis NIP7 homolog [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3977020.1 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
A4QND5	60S ribosome subunit biogenesis protein NIP7 homolog OS=Xenopus tropicalis OX=8364 GN=nip7 PE=2 SV=1
Q4T2X8	60S ribosome subunit biogenesis protein NIP7 homolog OS=Tetraodon nigroviridis OX=99883 GN=nip7 PE=3 SV=1
Q6DFH9	60S ribosome subunit biogenesis protein NIP7 homolog OS=Xenopus laevis OX=8355 GN=nip7 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007164 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03657 all species →	UPF0113	UPF0113 PUA domain	Domain	Interproscan
PF17833 all species →	UPF0113_N	UPF0113 Pre-PUA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005155 all species →	Domain	UPF0113, PUA domain	Interproscan
IPR016686 all species →	Family	Ribosome biogenesis factor, NIP7	Interproscan
IPR040598 all species →	Domain	60S ribosome subunit biogenesis protein NIP7, pre-PUA domain	Interproscan
IPR036974 all species →	Homologous_superfamily	PUA domain superfamily	Interproscan
IPR015947 all species →	Homologous_superfamily	PUA-like superfamily	Interproscan
IPR002478 all species →	Domain	PUA domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23415 all species →	CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT/60S RIBOSOME SUBUNIT BIOGENESIS PROTEIN NIP7	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0042255 all species →	Biological Process	ribosome assembly	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0030687 all species →	Cellular Component	preribosome, large subunit precursor	Interproscan
GO:0042273 all species →	Biological Process	ribosomal large subunit biogenesis	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
K07565	NIP7; 60S ribosome subunit biogenesis protein NIP7	-	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 CAB3977020.1 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

58.3Max TPM

12.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	28.41	58.33
apical branchlet · Temperature treatment at T0	6	4	12.36	35.39
apical branchlet · Temperature treatment at T25	5	2	1.92	5.09
apical branchlet · Control at T0	4	1	1.12	4.48

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	58.33
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	45.99
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	42.32
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	15.81
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.00
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	35.39
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	34.03
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.07
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.68
SRR19977426	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	5.09
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	4.50
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	4.48
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.