TkA01G098200 | RubberDandelionOmics

Gene overview

TkA01G098200

Reference: TK1151 Chr: Chr01 Coordinates: 24805253-24809239 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1441 bp · TkA01G098200|TK1151|cDNA

TTTACCTAATATCTAAGAAAGAAATAACTGTCGATTGAATACTTGAATTGCCTCAGAGTGTCGGTGAACAGAAGTCCACAAAATTGGTTTTGGATTAAAACGAACGATCATTAATGGGGAACCATAACTCCGGCGGGCGCCACCACCTACGAAACCGTAGAAATGGTGAACCAGTAGTCCAGAACCCTCAATATTACTACGGAACTCCATCAGATCTCCCACCACAAAACCCGGCGAGCTCAATCACGCATAACGAAATG...

CDS

Download CDS FASTA

1194 bp · TkA01G098200|TK1151|CDS

ATGTCTTCGTCATCGTCTTCGTCTTCGTCATCGTCGGATGACGATTTTGACGATTTTATATTTGATATGATGATAAAAATCTACTCGCACGTCCTACGTCGAGTGAACCAGAACTCCGCTGGGCGCCACCGCCGACGAAACCGAAGAAATGCTTCATCAGATTCAGATGCCGCACCACAAATCCCGGCGAGCTCAAGTAGGCATAACGAAATGGAAGCAGTATCACTTCCTTACTCCCAAGTTGATTGCAATTTGCGAGC...

Protein

Download Protein FASTA

397 aa · TkA01G098200|TK1151|PROTEIN

MSSSSSSSSSSSDDDFDDFIFDMMIKIYSHVLRRVNQNSAGRHRRRNRRNASSDSDAAPQIPASSSRHNEMEAVSLPYSQVDCNLRALAGQAEGFGRFAVGGLHGPLYHVTTLSDDGPGSLRVGCRKQEPQWIVFEVSGTIALSSYINVSSHKTIDGRGQRIKLTGKGLRLKQCEHVIICNLQFEGGRGHDVDAIQINPNSKHIWIDRCTLKDYDDSLINITRQSTNITISRCYFSNHDKAMLIGGDPSHHGDRCMCVTI...

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	`TkA01G098200`
TK1151 ID	TkA01G098200
OH-1004 ID	LXL04_004904
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	97.600
Protein coverage (%)	TK1151 96.222 / OH-1004 49.935 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 TkA01G098200

Location Chr01:24805253-24809239 (+)

Description Similar to At1g30350: Probable pectate lyase 4

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
`At5g63180`	Probable pectate lyase 22.	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_004904 · 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:0045490 pectin catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0030570 pectate lyase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G30350

ath:AT5G55720

sly:101253756

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.

Cytoplasm0.451

Rank 1 · TkA01G098200 · TK1151

Nucleus0.278

Rank 2 · TkA01G098200 · TK1151

Extracellular0.172

Rank 3 · TkA01G098200 · TK1151

Mitochondrion0.131

Rank 4 · TkA01G098200 · TK1151

Cell membrane0.109

Rank 5 · TkA01G098200 · 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.

PF28613HAC6_helical12-35 aa

PF00544Pectate_lyase_4145-317 aa

PF13229Beta_helix155-244 aa

PF13229Beta_helix280-340 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G098200	`PF28613`	HAC6_helical	12	35	0.031	14.8
TkA01G098200	`PF00544`	Pectate_lyase_4	145	317	2.8e-27	96.4
TkA01G098200	`PF13229`	Beta_helix	155	244	1.8e-05	25.1
TkA01G098200	`PF13229`	Beta_helix	280	340	1.8e-05	25.1

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q93Z04`	Arabidopsis thaliana	sp\|Q93Z04\|PLY13_ARATH Probable pectate lyase 13	37.400%	Swiss-Prot	Medium
`Q93Z25`	Arabidopsis thaliana	sp\|Q93Z25\|PLY22_ARATH Probable pectate lyase 22	32.900%	Swiss-Prot	Medium
`Q9C5M8`	Arabidopsis thaliana	sp\|Q9C5M8\|PLY18_ARATH Probable pectate lyase 18	36.800%	Swiss-Prot	Medium

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