LXL04_024954 | RubberDandelionOmics

Gene overview

LXL04_024954

Reference: OH-1004 Chr: Chr05 Coordinates: 102714567-102717387 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1764 bp · LXL04_024954|LXL04_024954|OH1004|cDNA

ATGTCAATGGGAGACGAACCTTTGTACCCAATAGCAGTACTAATCGATGAACTGAAGAATGACGACATCCAATTGCGTTTAAATTCCATCAGAAGACTATCAACAATCGCACGTGCACTAGGGGAAGAACGCACTCGAAAGGAGTTAATCCCTTTCTTGAGTGAAAacaatgatgatgatgatgaagttCTTCTTGCCATGGCAGAAGAGTTAGGTGTGTTCATTCCTTATGTTGGAGGAGTTGACCATGCCAATGTTCT...

CDS

Download CDS FASTA

1764 bp · LXL04_024954|LXL04_024954|OH1004|CDS

ATGTCAATGGGAGACGAACCTTTGTACCCAATAGCAGTACTAATCGATGAACTGAAGAATGACGACATCCAATTGCGTTTAAATTCCATCAGAAGACTATCAACAATCGCACGTGCACTAGGGGAAGAACGCACTCGAAAGGAGTTAATCCCTTTCTTGAGTGAAAACAATGATGATGATGATGAAGTTCTTCTTGCCATGGCAGAAGAGTTAGGTGTGTTCATTCCTTATGTTGGAGGAGTTGACCATGCCAATGTTCT...

Protein

Download Protein FASTA

587 aa · LXL04_024954|LXL04_024954|OH1004|PROTEIN

MSMGDEPLYPIAVLIDELKNDDIQLRLNSIRRLSTIARALGEERTRKELIPFLSENNDDDDEVLLAMAEELGVFIPYVGGVDHANVLLPPLETLCTVEETCVREKAVESLCRIGSQMKDTNLVEFFVPLVKRLAAGEWFTARVSACGLFHIAYPSAPDALKAELRSVYSQLCQDDMPMVRRSAATNLGKFAATMEPAHLKTEIMQIFEDLTQDDQDSVRLLAVEGCAALGKLLEPQDCVAHILPVIVNFSQDKSWRVRYM...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_024954`
TK1151 ID	TkA06G094270
OH-1004 ID	LXL04_024954
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 33.049 / OH-1004 33.049 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_024954

Location Chr05:102714567-102717387 (-)

Description Similar to PP2AA2: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g25800`	The A subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit.	Disparate roles for the regulatory A subunit isoforms in Arabidopsis protein phosphatase 2A.2004 · DOI: 10.1105/tpc.018994
`At1g13320`	The A subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit.	Disparate roles for the regulatory A subunit isoforms in Arabidopsis protein phosphatase 2A.2004 · DOI: 10.1105/tpc.018994
`At1g25490`	The A subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit.	The RCN1-encoded A subunit of protein phosphatase 2A increases phosphatase activity in vivo.1999 · DOI: 10.1046/j.1365-313x.1999.00607.x The Arabidopsis eer1 mutant has enhanced ethylene responses in the hypocotyl and stem.2001 · DOI: 10.1104/pp.125.2.1061 Genetic and chemical reductions in protein phosphatase activity alter auxin transport, gravity response, and lateral root growth.2001 · DOI: 10.1105/tpc.010158 Disruption of a guard cell-expressed protein phosphatase 2A regulatory subunit, RCN1, confers abscisic acid insensitivity in Arabidopsis.2002 · DOI: 10.1105/tpc.003335 Enhanced ethylene responsiveness in the Arabidopsis eer1 mutant results from a loss-of-function mutation in the protein phosphatase 2A A regulatory subunit, RCN1.2003 · DOI: 10.1046/j.1365-313x.2003.01762.x Disparate roles for the regulatory A subunit isoforms in Arabidopsis protein phosphatase 2A.2004 · DOI: 10.1105/tpc.018994 A mutation in protein phosphatase 2A regulatory subunit A affects auxin transport in Arabidopsis.1996 · PMID: 8641277

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024954 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006952 defense response Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0009926 auxin polar transport Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0042325 regulation of phosphorylation Biological Process

GO:0000159 protein phosphatase type 2A complex Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G13320

ath:AT1G25490

ath:AT3G25800

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Cytoplasm0.708

Rank 1 · LXL04_024954 · OH-1004

Nucleus0.304

Rank 2 · LXL04_024954 · OH-1004

Golgi apparatus0.165

Rank 3 · LXL04_024954 · OH-1004

Cell membrane0.131

Rank 4 · LXL04_024954 · OH-1004

Lysosome / Vacuole0.124

Rank 5 · LXL04_024954 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF20168.5PDS588-268 aa

PF01602.27Adaptin_N100-419 aa

PF29896.1PPFR1_M163-237 aa

PF22956.3PIK3R4-like_middle195-303 aa

PF13646.13HEAT_2210-301 aa

PF02985.29HEAT242-271 aa

PF29896.1PPFR1_M247-314 aa

PF30357.1RELCH_N258-370 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024954	`PF20168.5`	PDS5	88	268	1.9e-11	43.3
LXL04_024954	`PF01602.27`	Adaptin_N	100	419	6.7e-07	29.0
LXL04_024954	`PF29896.1`	PPFR1_M	163	237	4e-52	175.8
LXL04_024954	`PF22956.3`	PIK3R4-like_middle	195	303	4.9e-26	92.0
LXL04_024954	`PF13646.13`	HEAT_2	210	301	8.4e-30	103.6
LXL04_024954	`PF02985.29`	HEAT	242	271	2.4e-54	176.8
LXL04_024954	`PF29896.1`	PPFR1_M	247	314	4e-52	175.8
LXL04_024954	`PF30357.1`	RELCH_N	258	370	7.2e-21	75.8
LXL04_024954	`PF25757.2`	TPR_DNAAF5	275	421	3.7e-08	33.6
LXL04_024954	`PF22646.3`	PPP2R1A-like_HEAT	277	351	1.4e-46	157.5
LXL04_024954	`PF22956.3`	PIK3R4-like_middle	281	347	4.9e-26	92.0
LXL04_024954	`PF29896.1`	PPFR1_M	322	385	4e-52	175.8
LXL04_024954	`PF22956.3`	PIK3R4-like_middle	343	424	4.9e-26	92.0
LXL04_024954	`PF22646.3`	PPP2R1A-like_HEAT	353	421	1.4e-46	157.5
LXL04_024954	`PF13646.13`	HEAT_2	361	460	8.4e-30	103.6
LXL04_024954	`PF30359.1`	RELCH_C	527	585	4.2e-16	59.7

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q38950`	Arabidopsis thaliana	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform	90.460%	Swiss-Prot	strong database homology
`Q38951`	Arabidopsis thaliana	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A gamma isoform	88.416%	Swiss-Prot	strong database homology
`Q38845`	Arabidopsis thaliana	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	86.575%	Swiss-Prot	strong database homology

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