TkA05G339870 | RubberDandelionOmics

Gene overview

TkA05G339870

Reference: TK1151 Chr: Chr05 Coordinates: 84035690-84038614 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1649 bp · TkA05G339870|TK1151|cDNA

CTCACGTATATAAATAAATATACGATTTGACTGATTAACATTTTACAAGATGCCATGAAGGCGAATCACTGTGGTTCGGTTTCCCCAGTGGTTCCCTTTTGCAATCATATGCCTTTTTTCTTCTTGGCTTTTGTCCTCGTTGTCCCGCCTGTTCTAGCCGGGACAATGAAGAAAAATGTTGGTATTGCACATTTAGACGGCTTCGTTAAAGAACGCATTCACAATGCGACCAAGATGGCCATAAAGTCGTATAATCCTGA...

CDS

Download CDS FASTA

1362 bp · TkA05G339870|TK1151|CDS

ATGAAGGCGAATCACTGTGGTTCGGTTTCCCCAGTGGTTCCCTTTTGCAATCATATGCCTTTTTTCTTCTTGGCTTTTGTCCTCGTTGTCCCGCCTGTTCTAGCCGGGACAATGAAGAAAAATGTTGGTATTGCACATTTAGACGGCTTCGTTAAAGAACGCATTCACAATGCGACCAAGATGGCCATAAAGTCGTATAATCCTGACCCTGAATTGGTGGTCAACAATTTCAACAAACAAGTCCACGAGTCTTTTGAAGG...

Protein

Download Protein FASTA

453 aa · TkA05G339870|TK1151|PROTEIN

MKANHCGSVSPVVPFCNHMPFFFLAFVLVVPPVLAGTMKKNVGIAHLDGFVKERIHNATKMAIKSYNPDPELVVNNFNKQVHESFEGTNSTRRNLKGKKCMATNPIDRCWRCKKNWANHRQDLAKCVRGFGEHTRGGMGGRIYVVTDSSDHDVLTPKKGTLRYGVIQDKPLWIIFERPMVITLKEELMINHDKTIDGRGVIVHIAYGAGLTIQFVHNVIVHGIRIHHIVSKNGGYIRDSLAHFGLRTVSDGDGISIFGAS...

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	`TkA05G339870`
TK1151 ID	TkA05G339870
OH-1004 ID	LXL04_021000
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
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

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Basic Information and Functional Annotation

Gene ID TkA05G339870

Location Chr05:84035690-84038614 (+)

Description Similar to Pectate lyase

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g15110`	Probable pectate lyase 19.	No verified direct reference in this release
`At1g14420`	Probable pectate lyase that may be involved in pollen tube growth.	Two Arabidopsis late pollen transcripts are detected in cytoplasmic granules.2017 · DOI: 10.1002/pld3.12
`At3g01270`	Probable pectate lyase 7.	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_021000 · 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:0009664 plant-type cell wall organization Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0030570 pectate lyase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G14420

ath:AT3G01270

ath:AT5G15110

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.

Extracellular0.380

Rank 1 · TkA05G339870 · TK1151

Lysosome / Vacuole0.286

Rank 2 · TkA05G339870 · TK1151

Cytoplasm0.139

Rank 3 · TkA05G339870 · TK1151

Endoplasmic reticulum0.106

Rank 4 · TkA05G339870 · TK1151

Golgi apparatus0.099

Rank 5 · TkA05G339870 · 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.

PF04431Pec_lyase_N44-95 aa

PF13229Beta_helix67-100 aa

PF00544Pectate_lyase_4186-381 aa

PF13229Beta_helix215-298 aa

PF02241MCR_beta325-383 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G339870	`PF04431`	Pec_lyase_N	44	95	8.7e-16	58.7
TkA05G339870	`PF13229`	Beta_helix	67	100	0.0038	17.6
TkA05G339870	`PF00544`	Pectate_lyase_4	186	381	1.1e-18	68.1
TkA05G339870	`PF13229`	Beta_helix	215	298	0.0038	17.6
TkA05G339870	`PF02241`	MCR_beta	325	383	0.18	12.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LFP5`	Arabidopsis thaliana	sp\|Q9LFP5\|PLY19_ARATH Probable pectate lyase 19	50.700%	Swiss-Prot	High
`Q9M9S2`	Arabidopsis thaliana	sp\|Q9M9S2\|PLY3_ARATH Probable pectate lyase 3	53.700%	Swiss-Prot	High
`Q9SRH4`	Arabidopsis thaliana	sp\|Q9SRH4\|PLY7_ARATH Probable pectate lyase 7	51.100%	Swiss-Prot	High

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