LXL04_001354 | RubberDandelionOmics

Gene overview

LXL04_001354

Reference: OH-1004 Chr: Chr01 Coordinates: 24622422-24624785 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2184 bp · LXL04_001354|LXL04_001354|OH1004|cDNA

ATGAGAAAGTCATCACAAATATCTGAAATTGTTTGTTACCCACAAAATGGACTAGATGAACCGGCAGAGGCATGGGGTGTCCAGGTACATCCCCTCTTACAGCTTCATCAAACGAACACGCCTTCTTCAATCTTCTCCATCGTCAATCGCCTCCATCGTCTATGCCCATTGTCCTCTCTCTTTCAGTTCATACTCCTCATTTACTCCTCCAAATTCATCCATAATTCGTCCTTAATTCATTTCCAGAAAaaggtttttgg...

CDS

Download CDS FASTA

2184 bp · LXL04_001354|LXL04_001354|OH1004|CDS

ATGAGAAAGTCATCACAAATATCTGAAATTGTTTGTTACCCACAAAATGGACTAGATGAACCGGCAGAGGCATGGGGTGTCCAGGTACATCCCCTCTTACAGCTTCATCAAACGAACACGCCTTCTTCAATCTTCTCCATCGTCAATCGCCTCCATCGTCTATGCCCATTGTCCTCTCTCTTTCAGTTCATACTCCTCATTTACTCCTCCAAATTCATCCATAATTCGTCCTTAATTCATTTCCAGAAAAAGGTTTTTGG...

Protein

Download Protein FASTA

727 aa · LXL04_001354|LXL04_001354|OH1004|PROTEIN

MRKSSQISEIVCYPQNGLDEPAEAWGVQVHPLLQLHQTNTPSSIFSIVNRLHRLCPLSSLFQFILLIYSSKFIHNSSLIHFQKKVFGFFSFRNPKSHVPASLLPITVAVIVSVIVTSLKTFFFLEAQKSKHMSRASRSDVSLGFFPHSSHHSHLSDESISFQIDSSFRSSSRHAVPLQLMEEQTTTKINSVDLNGKTKIGGEEDEEERDIDNFQILGHHMFLKRRRDDNSSGATPESSSSSSTSSKRCRTDQSGQERSLE...

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_001354`
TK1151 ID	TkA01G544280
OH-1004 ID	LXL04_001354
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_001354

Location Chr01:24622422-24624785 (+)

Description Similar to SHM6: Serine hydroxymethyltransferase 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g22020`	Catalyzes the interconversion of serine and glycine.	No verified direct reference in this release
`At1g36370`	Catalyzes the interconversion of serine and glycine.	No verified direct reference in this release
`At4g13930`	Catalyzes the interconversion of serine and glycine with the conversion of tetrahydrofolate (THF) into 5,10-methylene-THF.	No verified direct reference in this release
`At4g13890`	Catalyzes the interconversion of serine and glycine.	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_001354 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006730 one-carbon metabolic process Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009555 pollen development Biological Process

GO:0010197 polar nucleus fusion Biological Process

GO:0019264 glycine biosynthetic process from L-serine Biological Process

GO:0035999 tetrahydrofolate interconversion Biological Process

GO:0046500 S-adenosylmethionine metabolic process Biological Process

GO:0046653 tetrahydrofolate metabolic process Biological Process

GO:0046686 response to cadmium ion Biological Process

GO:0055063 sulfate ion homeostasis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G22020

ath:AT1G36370

ath:AT4G13890

ath:AT4G13930

ddi:DDB_G0277947

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.

Cytoplasm0.364

Rank 1 · LXL04_001354 · OH-1004

Nucleus0.304

Rank 2 · LXL04_001354 · OH-1004

Plastid0.157

Rank 3 · LXL04_001354 · OH-1004

Mitochondrion0.150

Rank 4 · LXL04_001354 · OH-1004

Peroxisome0.065

Rank 5 · LXL04_001354 · 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.

PF00464.26SHMT274-674 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001354	`PF00464.26`	SHMT	274	674	9.1e-166	552.1

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
`Q9LM59`	Arabidopsis thaliana	Serine hydroxymethyltransferase 6	65.466%	Swiss-Prot	strong database homology
`Q84WV0`	Arabidopsis thaliana	Serine hydroxymethyltransferase 7	64.238%	Swiss-Prot	strong database homology
`O23254`	Arabidopsis thaliana	Serine hydroxymethyltransferase 4	62.473%	Swiss-Prot	moderate database homology
`Q9SVM4`	Arabidopsis thaliana	Serine hydroxymethyltransferase 5	60.738%	Swiss-Prot	moderate database homology

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