TkA08G429270 | RubberDandelionOmics

Gene overview

TkA08G429270

Reference: TK1151 Chr: Chr08 Coordinates: 109080236-109083900 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1475 bp · TkA08G429270|TK1151|cDNA

GATGCCCAAATTTGTACACAGGCCATTCCAACAACCTTACATATCTTCTCTAGGTAACAATATGGAAAATAGTTCTTTCAGTAATCCCAATCTTTATCCAAAACCCCAAAATCACAAAATGAAGGAATCAAACACCAAAAGGGGCTGGGTCGAGCAATCAGAATCCATACACTGTGGGGCAGTGGGGCTTCAAACTCATGATTCACGGTCCATGGCCTCACGCTTCATCATCCTAATTATACTGTGCTTTCAAGCTTCAA...

CDS

Download CDS FASTA

1371 bp · TkA08G429270|TK1151|CDS

ATGCCCAAATTTGTACACAGGCCATTCCAACAACCTTACATATCTTCTCTAGGTAACAATATGGAAAATAGTTCTTTCAGTAATCCCAATCTTTATCCAAAACCCCAAAATCACAAAATGAAGGAATCAAACACCAAAAGGGGCTGGGTCGAGCAATCAGAATCCATACACTGTGGGGCAGTGGGGCTTCAAACTCATGATTCACGGTCCATGGCCTCACGCTTCATCATCCTAATTATACTGTGCTTTCAAGCTTCAAT...

Protein

Download Protein FASTA

456 aa · TkA08G429270|TK1151|PROTEIN

MPKFVHRPFQQPYISSLGNNMENSSFSNPNLYPKPQNHKMKESNTKRGWVEQSESIHCGAVGLQTHDSRSMASRFIILIILCFQASISHAVYYNAPKPITTYTKNLAVNTIDACRRKTSNWAYNRRALADCAVGFGKGAIGGKSGPTYVVTNPTDDPINPKPGTLRYGVIQTKPLWIVFAKDMVIKLKNELIINSYKTIDGRGAKVEIAYGPCITIQHVSHVIIHGISIHDCKPGKSGLVRSSPTHLGHRQGSDGDAIDI...

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	`TkA08G429270`
TK1151 ID	TkA08G429270
OH-1004 ID	LXL04_020825
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	60.600
Protein coverage (%)	TK1151 76.316 / OH-1004 87.250 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 TkA08G429270

Location Chr08:109080236-109083900 (-)

Description Similar to At5g63180: Probable pectate lyase 22

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g11920`	Putative pectate lyase 2.	No verified direct reference in this release
`At4g22080`	Probable pectate lyase 16.	No verified direct reference in this release
`At4g22090`	Putative pectate lyase 17.	No verified direct reference in this release
`At1g30350`	Probable pectate lyase 4.	No verified direct reference in this release
`At1g67750`	Probable pectate lyase 5.	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_020825 · 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:0009624 response to nematode Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0030570 pectate lyase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G67750

ath:AT3G27400

ath:AT4G13710

ath:AT4G24780

ath:AT5G63180

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.

Extracellular0.504

Rank 1 · TkA08G429270 · TK1151

Lysosome / Vacuole0.191

Rank 2 · TkA08G429270 · TK1151

Cytoplasm0.123

Rank 3 · TkA08G429270 · TK1151

Endoplasmic reticulum0.090

Rank 4 · TkA08G429270 · TK1151

Cell membrane0.070

Rank 5 · TkA08G429270 · 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.

PF13229Beta_helix18-70 aa

PF00544Pectate_lyase_4188-395 aa

PF13229Beta_helix214-304 aa

PF13229Beta_helix217-305 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G429270	`PF13229`	Beta_helix	18	70	0.036	14.4
TkA08G429270	`PF00544`	Pectate_lyase_4	188	395	7.2e-29	101.6
TkA08G429270	`PF13229`	Beta_helix	214	304	0.036	14.4
TkA08G429270	`PF13229`	Beta_helix	217	305	0.036	14.4

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
`O65388`	Arabidopsis thaliana	sp\|O65388\|PLY2_ARATH Putative pectate lyase 2	69.500%	Swiss-Prot	High
`O65456`	Arabidopsis thaliana	sp\|O65456\|PLY16_ARATH Probable pectate lyase 16	66.900%	Swiss-Prot	High
`O65457`	Arabidopsis thaliana	sp\|O65457\|PLY17_ARATH Putative pectate lyase 17	66.700%	Swiss-Prot	High
`Q9C8G4`	Arabidopsis thaliana	sp\|Q9C8G4\|PLY4_ARATH Probable pectate lyase 4	58.100%	Swiss-Prot	High
`Q9FXD8`	Arabidopsis thaliana	sp\|Q9FXD8\|PLY5_ARATH Probable pectate lyase 5	54.300%	Swiss-Prot	High

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