LXL04_001578 | RubberDandelionOmics

Gene overview

LXL04_001578

Reference: OH-1004 Chr: Chr01 Coordinates: 29359238-29362678 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1932 bp · LXL04_001578|LXL04_001578|OH1004|cDNA

ATGGCGGCTTCAGCTTCATCTAGCCTTCTTTCATCTCGATCGCCCCTGAAATTAACCTCTCTATCTTCCCTCAGATGGAAATTACCTGTGTCAGTGGCGCTCCCTCGCCACCAACGACGCCGCGCCTCTCCGGTGTTCGTCGTTGTATCCATGGACGCCAAACCTACCGTCCTTGTCGCTGAAAAGCTAGGAGAAGCTGGACTTGATCTATTGAAAAGCTTTGCTAATGTTGATTGCTCGTATAACTTGAGTCCTGAGGA...

CDS

Download CDS FASTA

1932 bp · LXL04_001578|LXL04_001578|OH1004|CDS

ATGGCGGCTTCAGCTTCATCTAGCCTTCTTTCATCTCGATCGCCCCTGAAATTAACCTCTCTATCTTCCCTCAGATGGAAATTACCTGTGTCAGTGGCGCTCCCTCGCCACCAACGACGCCGCGCCTCTCCGGTGTTCGTCGTTGTATCCATGGACGCCAAACCTACCGTCCTTGTCGCTGAAAAGCTAGGAGAAGCTGGACTTGATCTATTGAAAAGCTTTGCTAATGTTGATTGCTCGTATAACTTGAGTCCTGAGGA...

Protein

Download Protein FASTA

643 aa · LXL04_001578|LXL04_001578|OH1004|PROTEIN

MAASASSSLLSSRSPLKLTSLSSLRWKLPVSVALPRHQRRRASPVFVVVSMDAKPTVLVAEKLGEAGLDLLKSFANVDCSYNLSPEELCTKISLCDALIVRSGTKVSREVFESSGGRLKVVGRAGVGIDNVDLGAATEHGCLVVNAPTANTVAAAEHGIALLTAMARNVAQADASVKAGKWQRNKYVGVSLVGKTLAVMGFGKVGTEVARRAKGLGMHVIAHDPYAPADRAHAIGVDLVSFDEAISTADFLSLHMPLTPA...

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_001578`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_001578

Location Chr01:29359238-29362678 (+)

Description Similar to PGDH1: D-3-phosphoglycerate dehydrogenase 1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34200`	Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB).	Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis.2013 · DOI: 10.1104/pp.113.226720 Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis.2013 · DOI: 10.1105/tpc.113.118992
`At3g19480`	Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB).	No verified direct reference in this release
`At1g17745`	Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB).	Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis.2013 · DOI: 10.1104/pp.113.226720 Regulation of serine biosynthesis in Arabidopsis. Crucial role of plastidic 3-phosphoglycerate dehydrogenase in non-photosynthetic tissues.1999 · DOI: 10.1074/jbc.274.1.397

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001578 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000096 sulfur amino acid metabolic process Biological Process

GO:0006564 L-serine biosynthetic process Biological Process

GO:0009555 pollen development Biological Process

GO:0009561 megagametogenesis Biological Process

GO:0009643 photosynthetic acclimation Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

GO:0009570 chloroplast stroma Cellular Component

KEGG gene cross-reference

ath:AT1G17745

ath:AT3G19480

ath:AT4G34200

mja:MJ_1018

mth:MTH_970

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.

Plastid0.942

Rank 1 · LXL04_001578 · OH-1004

Mitochondrion0.083

Rank 2 · LXL04_001578 · OH-1004

Cytoplasm0.060

Rank 3 · LXL04_001578 · OH-1004

Peroxisome0.037

Rank 4 · LXL04_001578 · OH-1004

Nucleus0.028

Rank 5 · LXL04_001578 · 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.

PF00389.372-Hacid_dh57-366 aa

PF02826.262-Hacid_dh_C159-334 aa

PF19304.5PGDH_inter377-482 aa

PF01842.32ACT524-586 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001578	`PF00389.37`	2-Hacid_dh	57	366	5.2e-34	117.5
LXL04_001578	`PF02826.26`	2-Hacid_dh_C	159	334	5.8e-64	215.4
LXL04_001578	`PF19304.5`	PGDH_inter	377	482	3.3e-16	60.2
LXL04_001578	`PF01842.32`	ACT	524	586	1.2e-10	41.7

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
`O49485`	Arabidopsis thaliana	D-3-phosphoglycerate dehydrogenase 1, chloroplastic	82.403%	Swiss-Prot	strong database homology
`Q9LT69`	Arabidopsis thaliana	D-3-phosphoglycerate dehydrogenase 3, chloroplastic	81.305%	Swiss-Prot	strong database homology
`O04130`	Arabidopsis thaliana	D-3-phosphoglycerate dehydrogenase 2, chloroplastic	79.298%	Swiss-Prot	strong database homology

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