LXL04_012614 | RubberDandelionOmics

Gene overview

LXL04_012614

Reference: OH-1004 Chr: Chr03 Coordinates: 15631960-15633948 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1113 bp · LXL04_012614|LXL04_012614|OH1004|cDNA

ATGTCCGTCGCTACCATCGTTCCGGCCCCTCTCACATCCTCAAATATCCGATCACGTTCAATCATATCCCCGTCCTCCTTTTCTCCCATCAACCCCTTCAAATGCTCTACTTTTGCCCTCCAATTTAACACCGCCAAGCTCACAACTCCTCTCATCCGAAACCCTAACTTCCGATTCGGTGTCTCAGCAATGAGCGTAGCAGCTCAGGAAAATCTCTCTACGACCGCATTCCTCGATCGAAGAGAAAGCGGAGTTCTTCA...

CDS

Download CDS FASTA

1113 bp · LXL04_012614|LXL04_012614|OH1004|CDS

ATGTCCGTCGCTACCATCGTTCCGGCCCCTCTCACATCCTCAAATATCCGATCACGTTCAATCATATCCCCGTCCTCCTTTTCTCCCATCAACCCCTTCAAATGCTCTACTTTTGCCCTCCAATTTAACACCGCCAAGCTCACAACTCCTCTCATCCGAAACCCTAACTTCCGATTCGGTGTCTCAGCAATGAGCGTAGCAGCTCAGGAAAATCTCTCTACGACCGCATTCCTCGATCGAAGAGAAAGCGGAGTTCTTCA...

Protein

Download Protein FASTA

370 aa · LXL04_012614|LXL04_012614|OH1004|PROTEIN

MSVATIVPAPLTSSNIRSRSIISPSSFSPINPFKCSTFALQFNTAKLTTPLIRNPNFRFGVSAMSVAAQENLSTTAFLDRRESGVLHFVKYHGLGNDFIMVNNLDSTDPKVTPEQAAKLCDRNFGIGADGVIFAMPGHNGTDYTMRIFNSDGSEPEMCGNGVRCFAKFIADLNSSEGRQSFTVHTGAGLIVPEIQDDGQVKVDMGEPVLKASDVPTKIPPNVNESVVKAKMEVDGTNWNVTCVSMGNPHCVTFGTQANDN...

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_012614`
TK1151 ID	TkA02G549740
OH-1004 ID	LXL04_012614
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.900
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_012614

Location Chr03:15631960-15633948 (-)

Description Similar to DAPF: Diaminopimelate epimerase, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g53580`	Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os12g0567200`	Diaminopimelate epimerase, chloroplastic.	No verified direct reference in this release
`UniProt: A2ZLS4`	Putative diaminopimelate epimerase, chloroplastic.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012614 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009089 L-lysine biosynthetic process via diaminopimelate Biological Process

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0008837 diaminopimelate epimerase activity Molecular Function

KEGG gene cross-reference

ana:alr2048

ath:AT3G53580

dosa:Os12g0567200

syn:slr1665

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.

Plastid0.985

Rank 1 · LXL04_012614 · OH-1004

Mitochondrion0.030

Rank 2 · LXL04_012614 · OH-1004

Cytoplasm0.025

Rank 3 · LXL04_012614 · OH-1004

Peroxisome0.020

Rank 4 · LXL04_012614 · OH-1004

Nucleus0.015

Rank 5 · LXL04_012614 · 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.

PF01678.25DAP_epimerase88-209 aa

PF01678.25DAP_epimerase242-363 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012614	`PF01678.25`	DAP_epimerase	88	209	1.1e-71	239.2
LXL04_012614	`PF01678.25`	DAP_epimerase	242	363	1.1e-71	239.2

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
`Q9LFG2`	Arabidopsis thaliana	Diaminopimelate epimerase, chloroplastic	66.577%	Swiss-Prot	strong database homology
`Q2QNF7`	Oryza sativa subsp. japonica	Diaminopimelate epimerase, chloroplastic	73.651%	Swiss-Prot	strong database homology
`A2ZLS4`	Oryza sativa subsp. indica	Putative diaminopimelate epimerase, chloroplastic	73.333%	Swiss-Prot	strong database homology

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