TkA04G005200 | RubberDandelionOmics

Gene overview

TkA04G005200

Reference: TK1151 Chr: Chr04 Coordinates: 1237198-1241176 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2281 bp · TkA04G005200|TK1151|cDNA

CCCAACTCCGTTTAAAAGCTTTAGTCCACGTATATATAACGTTAGTGAGTGTATGCTAAAATCGTAACACTTCCTACCATGCAAACCAACAAACTCATTCCCTTTCTTCTCTCTGCCCTTTTCTTGTTTGCGTTTTTCATTTTTTCCATTCCCAAAATTATAAACCACCACCACTCACTTCCGCTATTTACACAAAATACACCTCTACACTTACACCTTCACAAACGCATCCAAACACAAACAGCGTATACACATTGCCA...

CDS

Download CDS FASTA

1695 bp · TkA04G005200|TK1151|CDS

ATGCAAACCAACAAACTCATTCCCTTTCTTCTCTCTGCCCTTTTCTTGTTTGCGTTTTTCATTTTTTCCATTCCCAAAATTATAAACCACCACCACTCACTTCCGCTATTTACACAAAATACACCTCTACACTTACACCTTCACAAACGCATCCAAACACAAACAGCGTATACACATTGCCACGGTTCCCTATACTACGACCTCTGTCATGAAACCCTCACCACCGTTCTACCGGACCTCCGATCAAAATCTCTCCCAGA...

Protein

Download Protein FASTA

564 aa · TkA04G005200|TK1151|PROTEIN

MQTNKLIPFLLSALFLFAFFIFSIPKIINHHHSLPLFTQNTPLHLHLHKRIQTQTAYTHCHGSLYYDLCHETLTTVLPDLRSKSLPEIITATINQTVNDVKSTDFNVTAIRRKLRNLNALEIRALDDCHSLFLETVSELTSAISVLNTTPYNKHNDLQTLLSASMTNQATCLDGFSFSKSRNKIRRYFHKSVRNISRQVSNSLALLKKMNGASKRKAEAFPEYGEMAGGYPRWVKKKERALLQAPVNETSYNLVVAKDGS...

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	`TkA04G005200`
TK1151 ID	TkA04G005200
OH-1004 ID	LXL04_037081
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA04G005200

Location Chr04:1237198-1241176 (-)

Description Similar to PME40: Probable pectinesterase/pectinesterase inhibitor 40

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g02320`	Acts in the modification of cell walls via demethylesterification of cell wall pectin.	No verified direct reference in this release
`At4g02300`	Acts in the modification of cell walls via demethylesterification of cell wall pectin.	No verified direct reference in this release
`At1g53830`	Acts in the modification of cell walls via demethylesterification of cell wall pectin.	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_037081 · 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:0042545 cell wall modification Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0050829 defense response to Gram-negative bacterium Biological Process

GO:0005576 extracellular region Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0004857 enzyme inhibitor activity Molecular Function

GO:0030599 pectinesterase activity Molecular Function

GO:0046910 pectinesterase inhibitor activity Molecular Function

KEGG gene cross-reference

ath:AT1G53830

ath:AT4G02300

ath:AT4G02320

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.

Extracellular0.369

Rank 1 · TkA04G005200 · TK1151

Cell membrane0.225

Rank 2 · TkA04G005200 · TK1151

Endoplasmic reticulum0.130

Rank 3 · TkA04G005200 · TK1151

Lysosome / Vacuole0.127

Rank 4 · TkA04G005200 · TK1151

Cytoplasm0.119

Rank 5 · TkA04G005200 · 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.

PF29295SlaA_N4-35 aa

PF29295SlaA_N56-177 aa

PF04043PMEI58-205 aa

PF26988DUF8314108-226 aa

PF01095Pectinesterase252-548 aa

PF29295SlaA_N287-310 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G005200	`PF29295`	SlaA_N	4	35	3.8	8.0
TkA04G005200	`PF29295`	SlaA_N	56	177	3.8	8.0
TkA04G005200	`PF04043`	PMEI	58	205	6e-24	85.7
TkA04G005200	`PF26988`	DUF8314	108	226	0.0095	16.7
TkA04G005200	`PF01095`	Pectinesterase	252	548	1.5e-140	467.8
TkA04G005200	`PF29295`	SlaA_N	287	310	3.8	8.0

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
`O81301`	Arabidopsis thaliana	sp\|O81301\|PME40_ARATH Probable pectinesterase/pectinesterase inhibitor 40	53.300%	Swiss-Prot	High
`O81415`	Arabidopsis thaliana	sp\|O81415\|PME39_ARATH Probable pectinesterase/pectinesterase inhibitor 39	53.000%	Swiss-Prot	High
`Q42534`	Arabidopsis thaliana	sp\|Q42534\|PME2_ARATH Pectinesterase 2	48.300%	Swiss-Prot	Medium

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