TkA04G461720 | RubberDandelionOmics

Gene overview

TkA04G461720

Reference: TK1151 Chr: Chr04 Coordinates: 116480290-116483119 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2609 bp · TkA04G461720|TK1151|cDNA

AGGGACCATTTATGAACTTAAGTCTAAATGATATGAGCCACACATCGGGTCATATATCCACCTACACCGGGTTTCGACAAACCCAACCGCAGCCTGCAACGTGTCCAGATACATCCCCCGCCCCTCTGTGTCTGCTTCGTCAAACCCACGCCATTCTATCAATCCTCCCTCATCTTCTCTCTTCTCTCTCCTCTCTCTCAATCCTTCGCCGTGTGCCAGCAAATTTCAGCGCAGCCGTTTCAATTTCGTGCATCATCATC...

CDS

Download CDS FASTA

1218 bp · TkA04G461720|TK1151|CDS

ATGGATTTGACCCGTGCTCACCAATCGAACCTCTCGTTAGGGTTTGTACCTCACTCTTCGCACAGTAGTCAAATAGCCAGCGACACTGTATCCTTTCAGATCGATTCGAGTTTTCGAAATCCTCCTCATCACCTCGTTTCCGGTGTTCCTCTTCAATTGATGGAGCAACAGACCACAGTCGAGAGCAAAAACGTCGATTTGAATGAGAAGCACCAGCAAGCGAACGCAGGGAGCATGGATTTGAATGAGGAGAGCAAAGA...

Protein

Download Protein FASTA

405 aa · TkA04G461720|TK1151|PROTEIN

MDLTRAHQSNLSLGFVPHSSHSSQIASDTVSFQIDSSFRNPPHHLVSGVPLQLMEQQTTVESKNVDLNEKHQQANAGSMDLNEESKDGENDDGEEFRILGHSMCLKRRRDSTPSCTTTDSASSQTLSKRSHTSPESRRQAVRAWGNQSLQAADPDIFDLLEKEKHRQYKGIELIASENFVCKAVMEALGSHVTNKYSEGMPGARFYTGNQYIDEIEILCCQRALVAFGLDSESWGVNVQPYSCTSANFAVYTGLLLPGDR...

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	`TkA04G461720`
TK1151 ID	TkA04G461720
OH-1004 ID	LXL04_038750
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	94.800
Protein coverage (%)	TK1151 92.593 / OH-1004 51.613 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

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA04G461720

Location Chr04:116480290-116483119 (-)

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
`At1g36370`	Catalyzes the interconversion of serine and glycine.	No verified direct reference in this release
`At1g22020`	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_038750 · 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: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.

Cytoplasm0.515

Rank 1 · TkA04G461720 · TK1151

Nucleus0.487

Rank 2 · TkA04G461720 · TK1151

Mitochondrion0.064

Rank 3 · TkA04G461720 · TK1151

Cell membrane0.056

Rank 4 · TkA04G461720 · TK1151

Endoplasmic reticulum0.053

Rank 5 · TkA04G461720 · TK1151

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.

PF12722Hid157-143 aa

PF01863YgjP-like77-173 aa

PF00464SHMT149-396 aa

PF01212Beta_elim_lyase324-395 aa

PF00266Aminotran_5336-395 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G461720	`PF12722`	Hid1	57	143	2.7	6.8
TkA04G461720	`PF01863`	YgjP-like	77	173	0.019	15.7
TkA04G461720	`PF00464`	SHMT	149	396	1e-108	364.2
TkA04G461720	`PF01212`	Beta_elim_lyase	324	395	0.15	12.1
TkA04G461720	`PF00266`	Aminotran_5	336	395	0.23	11.1

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q84WV0`	Arabidopsis thaliana	sp\|Q84WV0\|GLYC7_ARATH Serine hydroxymethyltransferase 7	61.200%	Swiss-Prot	High
`Q9LM59`	Arabidopsis thaliana	sp\|Q9LM59\|GLYC6_ARATH Serine hydroxymethyltransferase 6	61.400%	Swiss-Prot	High
`O23254`	Arabidopsis thaliana	sp\|O23254\|GLYC4_ARATH Serine hydroxymethyltransferase 4	69.000%	Swiss-Prot	Medium
`Q9SVM4`	Arabidopsis thaliana	sp\|Q9SVM4\|GLYC5_ARATH Serine hydroxymethyltransferase 5	65.900%	Swiss-Prot	Medium

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