Gene detail

Detailed information of CAB3998456.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3998456.1, Splicing factor 3B subunit 3, partial [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3998456.1 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
A0JN52	Splicing factor 3B subunit 3 OS=Bos taurus OX=9913 GN=SF3B3 PE=2 SV=1
Q15393	Splicing factor 3B subunit 3 OS=Homo sapiens OX=9606 GN=SF3B3 PE=1 SV=4
Q921M3	Splicing factor 3B subunit 3 OS=Mus musculus OX=10090 GN=Sf3b3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004110 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10433 all species →	MMS1_N	Mono-functional DNA-alkylating methyl methanesulfonate N-term	Repeat	Interproscan
PF03178 all species →	CPSF_A	CPSF A subunit region	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050358 all species →	Family	RSE1/DDB1/CFT1/CPSF1	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR018846 all species →	Domain	Cleavage/polyadenylation specificity factor, A subunit, N-terminal	Interproscan
IPR004871 all species →	Domain	Cleavage/polyadenylation specificity factor, A subunit, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10644 all species →	DNA REPAIR/RNA PROCESSING CPSF FAMILY	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005686 all species →	Cellular Component	U2 snRNP	Interproscan
GO:0030620 all species →	Molecular Function	U2 snRNA binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	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
K12830	SF3B3, SAP130, RSE1; splicing factor 3B subunit 3	-	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3998456.1 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

17TPM > 0

4Conditions

100.7Max TPM

24.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	41.92	97.40
apical branchlet · Temperature treatment at T0	6	4	25.20	100.74
apical branchlet · Temperature treatment at T25	5	5	17.08	26.32
apical branchlet · Control at T0	4	2	8.39	24.28

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	97.40
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	50.94
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	37.50
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	33.49
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	23.20
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	9.01
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	100.74
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	28.81
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	13.08
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	8.56
SRR19977426	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
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	26.32
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	18.12
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	17.70
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	12.08
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	11.16
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	24.28
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	9.28
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

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.