Gene detail

Detailed information of CAB4001967.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4001967.1, splicing factor 3A subunit 1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4001967.1 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
A2VDN6	Splicing factor 3A subunit 1 OS=Bos taurus OX=9913 GN=SF3A1 PE=2 SV=1
Q15459	Splicing factor 3A subunit 1 OS=Homo sapiens OX=9606 GN=SF3A1 PE=1 SV=1
Q8K4Z5	Splicing factor 3A subunit 1 OS=Mus musculus OX=10090 GN=Sf3a1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005100 (this species only)
Ubiquitin family	ULD\|UBL\|NEDD8 · all ubiquitin genes in this species
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_Other · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12230 all species →	PRP21_like_P	Pre-mRNA splicing factor PRP21 like protein	Family	Interproscan
PF00240 all species →	ubiquitin	Ubiquitin family	Domain	Interproscan
PF09004 all species →	ALKBH8_N	Alkylated DNA repair protein alkB homolog 8, N-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035563 all species →	Domain	Splicing factor 3A subunit 1, ubiquitin domain	Interproscan
IPR022030 all species →	Domain	Splicing factor 3A subunit 1, conserved domain	Interproscan
IPR000626 all species →	Domain	Ubiquitin-like domain	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan
IPR045146 all species →	Family	Splicing factor 3A subunit 1	Interproscan
IPR015095 all species →	Domain	Alkylated DNA repair protein AlkB, homologue 8, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15316 all species →	SPLICEOSOME ASSOCIATED PROTEIN 114/SWAP SPLICING FACTOR-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000381 all species →	Biological Process	regulation of alternative mRNA splicing, via spliceosome	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005686 all species →	Cellular Component	U2 snRNP	Interproscan
GO:0045292 all species →	Biological Process	mRNA cis splicing, via spliceosome	Interproscan
GO:0071004 all species →	Cellular Component	U2-type prespliceosome	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 spliceosome	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0016706 all species →	Molecular Function	2-oxoglutarate-dependent dioxygenase 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

No KEGG orthology assignment for CAB4001967.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4001967.1 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

15TPM > 0

4Conditions

46.6Max TPM

15.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	30.32	46.57
apical branchlet · Temperature treatment at T0	6	6	17.59	43.53
apical branchlet · Temperature treatment at T25	5	2	4.78	16.20
apical branchlet · Control at T0	4	1	5.10	20.38

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	46.57
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	35.13
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	34.42
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	33.85
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	16.41
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	15.56
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	43.53
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	22.24
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	16.32
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	14.38
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	7.03
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.02
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	16.20
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	7.72
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	20.38
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.