TkA04G042180 | RubberDandelionOmics

Gene overview

TkA04G042180

Reference: TK1151 Chr: Chr04 Coordinates: 11308101-11310630 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

879 bp · TkA04G042180|TK1151|cDNA

TTCAGCCCTAAATAACTTCGACCTCTACTCTGATACTCTCCCAGGTTTCCGAGTTTTCGATTTCGAAGTCCGTCAACGCATCACTCGATCATCACCTTTCCCATTTTGCATTCGGCTCTCTACTCTGTGTACAGGCTCCCCAAATCGAAACAGCCCACAGAAAGCAAGAAAAAAGGATAAAGCATGTTGGACATAAATCTATTTAGGGAGGAAAAAGGCAACAATCCAGAAATCATACGGGAATCTCAACGCCGAAGGTT...

CDS

Download CDS FASTA

354 bp · TkA04G042180|TK1151|CDS

ATGTTGGACATAAATCTATTTAGGGAGGAAAAAGGCAACAATCCAGAAATCATACGGGAATCTCAACGCCGAAGGTTTGCAAATGTTGAAATTGTTGATGAAGTTATTCATCTTGACAAGGAGTGGCGACAACGTCAATTTGAGCTGGAACAGTTGCGCAAAGACTTCAACAGGATTACCAAAGAAGTTGCTAAACTTAGGATTGCTGGGGAAGATGCAAGTTCCATGACAAAAAATATAGAGGAAAACAAGGACTCAAT...

Protein

Download Protein FASTA

117 aa · TkA04G042180|TK1151|PROTEIN

MLDINLFREEKGNNPEIIRESQRRRFANVEIVDEVIHLDKEWRQRQFELEQLRKDFNRITKEVAKLRIAGEDASSMTKNIEENKDSIAKKDTEVQKPVQHYIQIGVGWESCPRFSSC

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	`TkA04G042180`
TK1151 ID	TkA04G042180
OH-1004 ID	LXL04_036542
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.000
Protein coverage (%)	TK1151 82.051 / OH-1004 21.007 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 TkA04G042180

Location Chr04:11308101-11310630 (-)

Description Similar to Serine--tRNA ligase

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g27470`	Catalyzes the attachment of serine to tRNA(Ser) in a two-step reaction: serine is first activated by ATP to form Ser-AMP and then transferred to the acceptor end of tRNA(Ser).	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_036542 · 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:0002181 cytoplasmic translation Biological Process

GO:0006434 seryl-tRNA aminoacylation Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0045335 phagocytic vesicle Cellular Component

GO:0000049 tRNA binding Molecular Function

GO:0004828 serine-tRNA ligase activity Molecular Function

GO:0005524 ATP binding Molecular Function

KEGG gene cross-reference

ath:AT5G27470

cal:CAALFM_C302780WA

ddi:DDB_G0272660

spo:2542163

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.

Cytoplasm0.679

Rank 1 · TkA04G042180 · TK1151

Nucleus0.216

Rank 2 · TkA04G042180 · TK1151

Mitochondrion0.120

Rank 3 · TkA04G042180 · TK1151

Plastid0.094

Rank 4 · TkA04G042180 · TK1151

Peroxisome0.091

Rank 5 · TkA04G042180 · 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.

PF02403Seryl_tRNA_N1-96 aa

PF15035Rootletin9-83 aa

PF15717PCM1_C13-94 aa

PF02410RsfS14-81 aa

PF23875DUF722914-61 aa

PF03938OmpH17-100 aa

PF20700Mutator18-113 aa

PF06156YabA29-99 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G042180	`PF02403`	Seryl_tRNA_N	1	96	8.4e-23	81.4
TkA04G042180	`PF15035`	Rootletin	9	83	0.18	12.5
TkA04G042180	`PF15717`	PCM1_C	13	94	0.015	14.7
TkA04G042180	`PF02410`	RsfS	14	81	0.068	13.4
TkA04G042180	`PF23875`	DUF7229	14	61	0.1	13.5
TkA04G042180	`PF03938`	OmpH	17	100	0.092	13.7
TkA04G042180	`PF20700`	Mutator	18	113	0.0081	15.8
TkA04G042180	`PF06156`	YabA	29	99	0.0045	18.3
TkA04G042180	`PF12325`	TMF_TATA_bd	34	96	0.28	12.0

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
`Q39230`	Arabidopsis thaliana	sp\|Q39230\|SYSC_ARATH Serine--tRNA ligase, cytoplasmic	66.700%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card