Gene detail

Detailed information of CAB4032940.1 in Paramuricea clavata

Genomic Location: pcla8_s020561:585...2906
NR annotation: CAB4032940.1, low molecular weight phosphotyrosine phosphatase isoform X2 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A079338

acaaacAATGTCAATTCAATGTTATGAGTGGTAGGGTTTTTTATGTGAACTTGTCGACATTATCTCATGGCAATTTGACAATTAATGTCCAGAGTGACCATCCCAGTATCcgaatattgtatattattcaaatattgtATCAAAATACAATCCCAGCCAATGACGGTGATAAACAACAATAATTGTGAGTTTAAAATACAGGTACTAGTAAATATCGATCAACGTTATCTGGGGTGGGTGGGTGGTGAAATAATAATGTCGATTTGACTttatttgtggcaacatgaatatggaaatGCCCCCCTAATAAGattaacaattttatttaaaatgtcACACTGTACCTCAGTATAAACCTTAGTACACATGGAGTAACCTGCAAGCCTTTCCAGTTTCTTTTGTCTTGGTAAGCCTTTCGATTGACTCTTCCTGTTGCTTATTCGAGCCAAATGCATAGGTCTTGTCAACTCGGAGGGGCTGGATGCAGAACTAGACGCCTTCTTCGTTCCGCTACTCGCATCACGGTTGTTGCTAGATGGCCCAGGagagtccgccatcttggattttgctCGACTTCCGATCGACAATTTGTCAACGTTTATATCACCTCTGTCGCTGTTTTGTAACGAATAAAACACCTCTATAATTGCACGGAATCATTATTGCACGTTTGGTAGCGAAATACAGCGACGTTTATGTAAGAAAACCGTTATTTCCCCCCCAAAATCTTAGAATCTGTGATTTTATTCTTTGAAGCCTCGTTTTCAGCCAAAAATGCACATGTCTGTACGACGATCAGCGGCTACGTGCTTGTTAATCGTTATCGTCTAGCACTTCGTGGAATTCAAAGATGGCGACCAAAACAAAATCTGTTTTATTTATCTGTCTTGGGAATATATGCCGTTCGCCAATGGCAGAGTTTGTCTTTAAAGATATGGTGAAGAACTCGGGCCAGTCGGCTTCTTGGAGAATAGATAGCGCCGGTTTTGTGGACTGGAATGAGGGAAACAGCCCTGAAGAATTGGTTGAAATTGTTTTGTTAGAGAATTCCATACCAGTTGGCAAACACCGTGCAAGAAAAATCCAAAAGAGTGATTTTAATGACTTCGATTACATACTTTCGATGGATGAGGCCGTGATGGATAAGCTGGATAAGCAAAAACCAAAGGAAAGCAGAGCAAAACTTGAGTTGCTACGCCGGTATGATCCTGCACAAGAAATTTTCAAAGATCCGTATTGCGGAAGCAAGGCTGATTTTGAAAAAGTTTTGAGACAATGCAAACTTTGCTTAACTAATTTCCTGAAAGCAGTTGACAAGAATTAATGCACAATTTTAATGTTAAACTTTTGGCTTTAAAGAGTCGGTCATTTCAAGTCCGTTCAGCGGATGTGCCATTGCagagtttgtttacattttgaagacactatattcataaaatataatGCACTTAGTTAAAACTGTGCTTTGAAATGAATATAGATTGGAATTTCAATTTAGAATATGTCGAAATAACGCAAAATGTtggtatagacccattgcactgatgtcacaaatccttagagtgtcctccagatgctccctaacaatagtgagcttaagaTCCACGACGCGAGCGGCTCAACAacgcggtctgaatttcagctcaagaatgagcgttAGGCAATTTCATTACTGTAATTAATGTTTGAAGATTTTTCAAATAACATTACGAACTGCTAAGTTTGACtcaagcgatgcaatgtttgctgtaattttgactttaagtaacacctcttgggtcgcaataagctttcacgttgcttcaaagacgtgataatgcttagtttaacgttgtgCTGAGCATGACCAAGCTgttgagaatacccctgggaccacaagttattcacagtttttctcttgcatgaaaaatttctttctttcgcaagcgcgtcgttgagccggccgtcgtagatcttaaattcgctaatatctgttcgggtataacaaccacatacagcgcaaaaattaaccattttaatacaaaattattataaagttttacaaaatttgctttgattacgaaagttatattatgcacagattgctaatttgtccctGGGTCTGTTTTTCACCCCCAGAAGGTTCTCGCatagcacatgcgcagaacagacttgaTCTAATCTTTAATCAGCAGGACTTGAAccagggcttgaattttatcgcggcaattgccgtagagggaaaacaaaatgctgtggatcattgcggcaacgacggcaattttttgccgaaaACTATAATTTTTATTCTATTCACTAAATTACTATAATACTATATTAACA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P81693	Low molecular weight phosphotyrosine protein phosphatase OS=Sus scrofa OX=9823 GN=ACP1 PE=1 SV=2
P11064	Low molecular weight phosphotyrosine protein phosphatase OS=Bos taurus OX=9913 GN=ACP1 PE=1 SV=3
P24666	Low molecular weight phosphotyrosine protein phosphatase OS=Homo sapiens OX=9606 GN=ACP1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009609 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01451 all species →	LMWPc	Low molecular weight phosphotyrosine protein phosphatase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR023485 all species →	Domain	Phosphotyrosine protein phosphatase I	Interproscan
IPR017867 all species →	Family	Protein-tyrosine phosphatase, low molecular weight	Interproscan
IPR050438 all species →	Family	Low Molecular Weight Phosphotyrosine Protein Phosphatase	Interproscan
IPR036196 all species →	Homologous_superfamily	Phosphotyrosine protein phosphatase I superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11717 all species →	LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004725 all species →	Molecular Function	protein tyrosine phosphatase activity	Interproscan
GO:0006470 all species →	Biological Process	protein dephosphorylation	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
K14394	ACP1; low molecular weight phosphotyrosine protein phosphatase	EC:3.1.3.2 EC:3.1.3.48	Protein phosphatases and associated proteins	ko01009	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4032940.1 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

9TPM > 0

4Conditions

11.7Max TPM

1.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	2.21	5.10
apical branchlet · Temperature treatment at T0	6	3	2.52	11.73
apical branchlet · Temperature treatment at T25	5	1	0.30	1.50
apical branchlet · Control at T0	4	1	0.37	1.49

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	5.10
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.23
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.03
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	1.91
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	11.73
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.11
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.27
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977428	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	1.50
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
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	1.49
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.