LXL04_015997 | RubberDandelionOmics

Gene overview

LXL04_015997

Reference: OH-1004 Chr: Chr03 Coordinates: 102441535-102446133 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3180 bp · LXL04_015997|LXL04_015997|OH1004|cDNA

ATGGAATCTAAGCTGGATTGTGATGCGGATCAAGGTCATGATCCAAACCAAGGTTCCATGGCCAAGATAGAAGAGAATGGCAAGCGTCCAGTGGTATATATTTACAGACAAGATGTTGTAAAGAGCAAAATTGATGGTAAAACAGGGGTAGTCACAGAAGTTGCAGGTGATTCTGATTCAGATAGCAGTACcagtgatgatgatgatgatgaagatgaagatgaagagaaTGAAGACACTGAAACAGCGGGTCCCACTGA...

CDS

Download CDS FASTA

3180 bp · LXL04_015997|LXL04_015997|OH1004|CDS

ATGGAATCTAAGCTGGATTGTGATGCGGATCAAGGTCATGATCCAAACCAAGGTTCCATGGCCAAGATAGAAGAGAATGGCAAGCGTCCAGTGGTATATATTTACAGACAAGATGTTGTAAAGAGCAAAATTGATGGTAAAACAGGGGTAGTCACAGAAGTTGCAGGTGATTCTGATTCAGATAGCAGTACCAGTGATGATGATGATGATGAAGATGAAGATGAAGAGAATGAAGACACTGAAACAGCGGGTCCCACTGA...

Protein

Download Protein FASTA

1059 aa · LXL04_015997|LXL04_015997|OH1004|PROTEIN

MESKLDCDADQGHDPNQGSMAKIEENGKRPVVYIYRQDVVKSKIDGKTGVVTEVAGDSDSDSSTSDDDDDEDEDEENEDTETAGPTEDGSQDLNENITGNNTDNENDDEETTPLPADHVRVFWMDESQSTQSQNDVIVIDRGFLHGDYVASVSDPTGQVGVVVDVSISVDLSTIEGSVINDVSSKILKRVRDFQVGDYVILGPWLGRIDDVLDNVTVMFDDGSVCKVMKADPIQLKPVSKNNNNNNNNLLEDSHYPYYPG...

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_015997`
TK1151 ID	TkA02G277700
OH-1004 ID	LXL04_015997
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.100
Protein coverage (%)	TK1151 98.849 / OH-1004 96.695 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_015997

Location Chr03:102441535-102446133 (+)

Description Similar to UBC23: Probable ubiquitin-conjugating enzyme E2 23

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g16920`	Accepts the ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins.	No verified direct reference in this release
`At2g33770`	E2 ubiquitin-protein ligase that mediates E1-dependent protein ubiquitination.	PHO2-dependent degradation of PHO1 modulates phosphate homeostasis in Arabidopsis.2012 · DOI: 10.1105/tpc.112.096636 Nitrogen limitation adaptation, a target of microRNA827, mediates degradation of plasma membrane-localized phosphate transporters to maintain phosphate homeostasis in Arabidopsis.2013 · DOI: 10.1105/tpc.113.116012 Identification of downstream components of ubiquitin-conjugating enzyme PHOSPHATE2 by quantitative membrane proteomics in Arabidopsis roots.2013 · DOI: 10.1105/tpc.113.115998 NITROGEN LIMITATION ADAPTATION recruits PHOSPHATE2 to target the phosphate transporter PT2 for degradation during the regulation of Arabidopsis phosphate homeostasis.2014 · DOI: 10.1105/tpc.113.120311
`At3g15355`	Accepts the ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins.	No verified direct reference in this release
`At1g53025`	Accepts the ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins.	No verified direct reference in this release
`At1g53020`	Accepts the ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_015997 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006817 phosphate ion transport Biological Process

GO:0016036 cellular response to phosphate starvation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0055062 phosphate ion homeostasis Biological Process

GO:2000185 regulation of phosphate transmembrane transport Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005524 ATP binding Molecular Function

GO:0016874 ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G53025

ath:AT2G16920

ath:AT2G33770

ath:AT3G15355

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.

Cytoplasm0.501

Rank 1 · LXL04_015997 · OH-1004

Nucleus0.379

Rank 2 · LXL04_015997 · OH-1004

Cell membrane0.138

Rank 3 · LXL04_015997 · OH-1004

Golgi apparatus0.099

Rank 4 · LXL04_015997 · OH-1004

Lysosome / Vacuole0.091

Rank 5 · LXL04_015997 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

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

PF23048.2SH3-A_UBE2O34-135 aa

PF23046.2tSH3-B_UBE2O195-333 aa

PF23043.2SH3-B_UBE2O462-538 aa

PF23044.2SH3-C_UBE2O539-611 aa

PF00179.32UQ_con789-919 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015997	`PF23048.2`	SH3-A_UBE2O	34	135	1.7e-09	39.0
LXL04_015997	`PF23046.2`	tSH3-B_UBE2O	195	333	5.7e-44	149.9
LXL04_015997	`PF23043.2`	SH3-B_UBE2O	462	538	6.6e-18	65.6
LXL04_015997	`PF23044.2`	SH3-C_UBE2O	539	611	3e-10	40.5
LXL04_015997	`PF00179.32`	UQ_con	789	919	1e-19	71.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9ZVX1`	Arabidopsis thaliana	Probable ubiquitin-conjugating enzyme E2 23	58.279%	Swiss-Prot	strong database homology
`Q8VY10`	Arabidopsis thaliana	Probable ubiquitin-conjugating enzyme E2 24	39.083%	Swiss-Prot	moderate database homology
`Q9LUQ5`	Arabidopsis thaliana	Probable ubiquitin-conjugating enzyme E2 25	52.490%	Swiss-Prot	weak database homology
`Q8GY87`	Arabidopsis thaliana	Probable ubiquitin-conjugating enzyme E2 26	56.522%	Swiss-Prot	weak database homology
`Q9C918`	Arabidopsis thaliana	Putative ubiquitin-conjugating enzyme E2 38	56.332%	Swiss-Prot	weak database homology

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