TkA04G213760 | RubberDandelionOmics

Gene overview

TkA04G213760

Reference: TK1151 Chr: Chr04 Coordinates: 54712027-54715796 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1534 bp · TkA04G213760|TK1151|cDNA

CCATTTTTCATACCATTTAATTTCACAAAATGCATCTTCGCAAAACCAACATTCTCTTGGTTTGCCTTTTAACTTCTCTCTTATCTATCATTAAGGCCACTCTTAATCTCACGCTTCCGTATCAACACCCTAATCCTGAAGCTGTTGTTCAAGAAGTACAGAGGCAAGTAAATGTATCGATATATAGAAGAGAAATGCTGGACATCGGCGGCGGTTGTCTTACCGGAAACCCAATAGACGATTGCTGGAAGTGCGACCCG...

CDS

Download CDS FASTA

1479 bp · TkA04G213760|TK1151|CDS

ATGCATCTTCGCAAAACCAACATTCTCTTGGTTTGCCTTTTAACTTCTCTCTTATCTATCATTAAGGCCACTCTTAATCTCACGCTTCCGTATCAACACCCTAATCCTGAAGCTGTTGTTCAAGAAGTACAGAGGCAAGTAAATGTATCGATATATAGAAGAGAAATGCTGGACATCGGCGGCGGTTGTCTTACCGGAAACCCAATAGACGATTGCTGGAAGTGCGACCCGAACTGGGGCAACGACCGGCAACGCCTCGC...

Protein

Download Protein FASTA

492 aa · TkA04G213760|TK1151|PROTEIN

MHLRKTNILLVCLLTSLLSIIKATLNLTLPYQHPNPEAVVQEVQRQVNVSIYRREMLDIGGGCLTGNPIDDCWKCDPNWGNDRQRLADCGIGFGRFALGGKGGQYYIVTDSSDTDVINPAPGTLRYAVLLPEPLWIIFASSMLIKLKHELIVNSYKTIDGRGVNVAITGGGCITLQYVTNIIIHNIRVYDCKPSGNADIRSSPTHVGRRGLSDGDGISISGGRNIWIDHCSLSHCTDGLIDAILGSTAITISNSYFTHHN...

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	`TkA04G213760`
TK1151 ID	TkA04G213760
OH-1004 ID	LXL04_034794
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	98.000
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 TkA04G213760

Location Chr04:54712027-54715796 (+)

Description Similar to PMR6: Probable pectate lyase 13

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g54920`	Susceptibility factor required for infection by most powdery mildews, but not by unrelated pathogens.	PMR6, a pectate lyase-like gene required for powdery mildew susceptibility in Arabidopsis.2002 · DOI: 10.1105/tpc.003509
`At3g53190`	Probable pectate lyase 12.	No verified direct reference in this release
`At1g67750`	Probable pectate lyase 5.	No verified direct reference in this release
`At4g13710`	Probable pectate lyase 15.	No verified direct reference in this release
`At4g24780`	Probable pectate lyase 18.	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_034794 · 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:0042547 cell wall modification involved in multidimensional cell growth Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0098552 side of membrane Cellular Component

GO:0030570 pectate lyase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G04680

ath:AT1G67750

ath:AT3G53190

ath:AT3G54920

ath:AT4G13710

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.

Extracellular0.316

Rank 1 · TkA04G213760 · TK1151

Lysosome / Vacuole0.287

Rank 2 · TkA04G213760 · TK1151

Cytoplasm0.170

Rank 3 · TkA04G213760 · TK1151

Cell membrane0.152

Rank 4 · TkA04G213760 · TK1151

Endoplasmic reticulum0.137

Rank 5 · TkA04G213760 · 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.

PF23331VWC2L_C69-89 aa

PF00544Pectate_lyase_4147-356 aa

PF13229Beta_helix171-262 aa

PF23331VWC2L_C219-238 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G213760	`PF23331`	VWC2L_C	69	89	0.34	11.6
TkA04G213760	`PF00544`	Pectate_lyase_4	147	356	1.9e-22	80.5
TkA04G213760	`PF13229`	Beta_helix	171	262	0.004	17.5
TkA04G213760	`PF23331`	VWC2L_C	219	238	0.34	11.6

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
`Q93Z04`	Arabidopsis thaliana	sp\|Q93Z04\|PLY13_ARATH Probable pectate lyase 13	65.600%	Swiss-Prot	High
`Q9SCP2`	Arabidopsis thaliana	sp\|Q9SCP2\|PLY12_ARATH Probable pectate lyase 12	60.800%	Swiss-Prot	High
`Q9FXD8`	Arabidopsis thaliana	sp\|Q9FXD8\|PLY5_ARATH Probable pectate lyase 5	64.600%	Swiss-Prot	High
`Q944R1`	Arabidopsis thaliana	sp\|Q944R1\|PLY15_ARATH Probable pectate lyase 15	61.700%	Swiss-Prot	High
`Q9C5M8`	Arabidopsis thaliana	sp\|Q9C5M8\|PLY18_ARATH Probable pectate lyase 18	62.400%	Swiss-Prot	High

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