TkA04G408500 | RubberDandelionOmics

Gene overview

TkA04G408500

Reference: TK1151 Chr: Chr04 Coordinates: 102704583-102707157 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1796 bp · TkA04G408500|TK1151|cDNA

ACCTAACTCTTGAAAAACCCTTGCTCCTATTTGGAGAGGAAATACTCGCCACTTCCTCGCTCTATTCCTTCATCAATGGCGGCGAATTCTCTTACACAACTTCAGTTCTCATCGCTTTCATTCGTCAAAACCCTAAATCATTCTTCAAAACCCATCACTCCCACTCCCACAACCTTAATTTCTCTTAAACCCGGTTCCAGAACACTCCTAATCCGAGCCGTCGTATCGCAAAAACCTACACAACCAACAGACATTCCAGC...

CDS

Download CDS FASTA

612 bp · TkA04G408500|TK1151|CDS

ATGGTGAAATTCATAGACGAAATTCGATCCCAAGGATTTGATATTAATTATTTAAATATCGGAGGTGGTCTAGGCATTGATTATTATCACACCGGTACCATTCTTCCTACCCCCCGCGATCTTATCGACACTGTGAGGGAGTTAGTTTTGTCGCGAAACCTTAATCTTATTATTGAACCTGGGAGGTCGTTAATTGCAAATACTTGTTGTCTTGTGAACCGTGTGACGGGTGTGAAAACAAATGGGACGAAAAACTTTAT...

Protein

Download Protein FASTA

203 aa · TkA04G408500|TK1151|PROTEIN

MVKFIDEIRSQGFDINYLNIGGGLGIDYYHTGTILPTPRDLIDTVRELVLSRNLNLIIEPGRSLIANTCCLVNRVTGVKTNGTKNFIVIDGSMAELIRPSLYDAYQHIELVSPPPSDSAVSTFDVVGPVCESADFLGKDRDLPAPASGSGLVVHDAGAYCMSMASTYNLKMRPPEYWVDEDGSVAKIRHGETFEDHMRYFEGL

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	`TkA04G408500`
TK1151 ID	TkA04G408500
OH-1004 ID	LXL04_023881
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	93.300
Protein coverage (%)	TK1151 100.000 / OH-1004 41.420 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	TK1151 / GWHBCHF00000000

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA04G408500

Location Chr04:102704583-102707157 (+)

Description Similar to LYSA1: Diaminopimelate decarboxylase 1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g14390`	Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.	No verified direct reference in this release
`At5g11880`	Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0440000`	Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_023881 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

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

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0008836 diaminopimelate decarboxylase activity Molecular Function

GO:0030170 pyridoxal phosphate binding Molecular Function

KEGG gene cross-reference

ath:AT3G14390

ath:AT5G11880

dosa:Os02g0440000

nme:NMB1976

pae:PA5277

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

Open Annotation Module

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.

Cytoplasm0.739

Rank 1 · TkA04G408500 · TK1151

Nucleus0.402

Rank 2 · TkA04G408500 · TK1151

Mitochondrion0.083

Rank 3 · TkA04G408500 · TK1151

Peroxisome0.057

Rank 4 · TkA04G408500 · TK1151

Cell membrane0.052

Rank 5 · TkA04G408500 · TK1151

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.

PF02784Orn_Arg_deC_N3-66 aa

PF00278Orn_DAP_Arg_deC67-157 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G408500	`PF02784`	Orn_Arg_deC_N	3	66	1.2e-07	32.0
TkA04G408500	`PF00278`	Orn_DAP_Arg_deC	67	157	9.9e-23	81.0

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
`Q949X7`	Arabidopsis thaliana	sp\|Q949X7\|DCDA1_ARATH Diaminopimelate decarboxylase 1, chloroplastic	83.700%	Swiss-Prot	High
`Q94A94`	Arabidopsis thaliana	sp\|Q94A94\|DCDA2_ARATH Diaminopimelate decarboxylase 2, chloroplastic	83.300%	Swiss-Prot	High
`Q6ZG77`	Oryza sativa subsp. japonica	sp\|Q6ZG77\|DCDA_ORYSJ Probable diaminopimelate decarboxylase, chloroplastic	79.300%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card