LXL04_038750 | RubberDandelionOmics

Gene overview

LXL04_038750

Reference: OH-1004 Chr: Chr09 Coordinates: 49519042-49521980 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2235 bp · LXL04_038750|LXL04_038750|OH1004|cDNA

ATGGTGGAGAAGAGGGAAGAAAGTAGGAAAAACAGGGAAGAGAAGAGGGAAGAAAACAGGggtaaaagaaaaagaaaagaaacagcgaacaaagcaaaaacaaaagaaacaaagaaacagATAGAGAGATCGTGCGAGGCAGGGAGAAAGATGAGACCGAGAATCAGTGAAAGGTCTGAGAAACATAAATATCAGggaccatttatgaacttaagtctAAATGATATGAGCCACACAGCGGGTCATATATCCACCTACAC...

CDS

Download CDS FASTA

2235 bp · LXL04_038750|LXL04_038750|OH1004|CDS

ATGGTGGAGAAGAGGGAAGAAAGTAGGAAAAACAGGGAAGAGAAGAGGGAAGAAAACAGGGGTAAAAGAAAAAGAAAAGAAACAGCGAACAAAGCAAAAACAAAAGAAACAAAGAAACAGATAGAGAGATCGTGCGAGGCAGGGAGAAAGATGAGACCGAGAATCAGTGAAAGGTCTGAGAAACATAAATATCAGGGACCATTTATGAACTTAAGTCTAAATGATATGAGCCACACAGCGGGTCATATATCCACCTACAC...

Protein

Download Protein FASTA

744 aa · LXL04_038750|LXL04_038750|OH1004|PROTEIN

MVEKREESRKNREEKREENRGKRKRKETANKAKTKETKKQIERSCEAGRKMRPRISERSEKHKYQGPFMNLSLNDMSHTAGHISTYTGFRQTQPQPATCPDTSPAPLCLLRQTHAILSILPHLLSSLSSLSILRRVPANFSAAVSISCIIITLRLVSKRFASIDIKSLGIRIDSSFRNPPHHLVSGVPLQLMEQQTTVESKNVDLNEKHQQANAGSMDLNEESKDGENDDGEEFRILGHSMCLKRRRDSTPSCTTTDSAS...

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_038750`
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_038750

Location Chr09:49519042-49521980 (-)

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

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Functional annotation source: OH1004 · LXL04_038750 · 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.

Cytoplasm0.477

Rank 1 · LXL04_038750 · OH-1004

Nucleus0.366

Rank 2 · LXL04_038750 · OH-1004

Mitochondrion0.118

Rank 3 · LXL04_038750 · OH-1004

Cell membrane0.084

Rank 4 · LXL04_038750 · OH-1004

Endoplasmic reticulum0.067

Rank 5 · LXL04_038750 · 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.

PF00464.26SHMT287-691 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038750	`PF00464.26`	SHMT	287	691	1.6e-163	544.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LM59`	Arabidopsis thaliana	Serine hydroxymethyltransferase 6	66.090%	Swiss-Prot	strong database homology
`Q84WV0`	Arabidopsis thaliana	Serine hydroxymethyltransferase 7	64.763%	Swiss-Prot	strong database homology
`O23254`	Arabidopsis thaliana	Serine hydroxymethyltransferase 4	63.226%	Swiss-Prot	moderate database homology
`Q9SVM4`	Arabidopsis thaliana	Serine hydroxymethyltransferase 5	62.151%	Swiss-Prot	moderate database homology

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