TkA03G042240 | RubberDandelionOmics

Gene overview

TkA03G042240

Reference: TK1151 Chr: Chr03 Coordinates: 11143099-11147690 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1878 bp · TkA03G042240|TK1151|cDNA

TAAAAGTCTTGAACACGTTTTTGCTCTACATCACTGATTTGTGAGGGCAACAAGCTCATCCACCGCCCCCACAACCAAATCTTTCTTGTCCCCGTTAAGAAACTAACAAATCGATCAAACTTCGCATCAAGTGATGGGTTACTGCTTCAGATCCTTCGCACGATTCTCCATTTCCACCATTGTTCTTGCCATCCTTCTTTCTTCGTCCAGTTTCACTTGCACAGAAGCCTATGATGCACTTGACCCAAATGGAAATATCA...

CDS

Download CDS FASTA

1350 bp · TkA03G042240|TK1151|CDS

ATGGGTTACTGCTTCAGATCCTTCGCACGATTCTCCATTTCCACCATTGTTCTTGCCATCCTTCTTTCTTCGTCCAGTTTCACTTGCACAGAAGCCTATGATGCACTTGACCCAAATGGAAATATCACAATCAAGTGGGACATCATTAGTTGGACTCCAGATGGCTATGTTGCGGTGGTCACTATGTACAACTTCCAACAATACCGCCACATTTCACCTCCAGGGTGGACCTTAGGGTGGACATGGGCTAAAAAAGAGGT...

Protein

Download Protein FASTA

449 aa · TkA03G042240|TK1151|PROTEIN

MGYCFRSFARFSISTIVLAILLSSSSFTCTEAYDALDPNGNITIKWDIISWTPDGYVAVVTMYNFQQYRHISPPGWTLGWTWAKKEVIWSMMGGQTTEQGDCSRYKTTPPHCCKKTPTVVDLLPGTPYNQQIANCCKGGVINSWAQEPNNYASSFQLSVGAAGTTNKTVKPPKNFTLLAPGPGYTCGPAVVGKPSKFVTPDGRRVTQAMMTWNVTCTYSQFLAQKTPTCCVSLSSFYNDTIVPCPTCTCGCQNNDTHPGS...

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	`TkA03G042240`
TK1151 ID	TkA03G042240
OH-1004 ID	LXL04_006492
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	98.200
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 TkA03G042240

Location Chr03:11143099-11147690 (-)

Description Similar to COB: Protein COBRA

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g60920`	Involved in determining the orientation of cell expansion, probably by playing an important role in cellulose deposition.	No verified direct reference in this release
`At3g02210`	COBRA-like protein 1.	No verified direct reference in this release
`At3g29810`	COBRA-like protein 2.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0386800`	Involved in determining the orientation of cell expansion, probably by playing an important role in cellulose deposition.	No verified direct reference in this release
`Os07g0604300`	Involved in determining the orientation of cell expansion, probably by playing an important role in cellulose deposition.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006492 · 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:0009651 response to salt stress Biological Process

GO:0009664 plant-type cell wall organization Biological Process

GO:0009825 multidimensional cell growth Biological Process

GO:0009832 plant-type cell wall biogenesis Biological Process

GO:0010214 seed coat development Biological Process

GO:0010215 cellulose microfibril organization Biological Process

GO:0048316 seed development Biological Process

GO:0048354 mucilage biosynthetic process involved in seed coat development Biological Process

GO:0052324 plant-type cell wall cellulose biosynthetic process Biological Process

GO:0005794 Golgi apparatus Cellular Component

GO:0005797 Golgi medial cisterna Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT3G02210

ath:AT3G29810

ath:AT5G60920

dosa:Os05g0386800

dosa:Os07g0604300

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.

Cell membrane0.812

Rank 1 · TkA03G042240 · TK1151

Cytoplasm0.092

Rank 2 · TkA03G042240 · TK1151

Extracellular0.085

Rank 3 · TkA03G042240 · TK1151

Endoplasmic reticulum0.066

Rank 4 · TkA03G042240 · TK1151

Lysosome / Vacuole0.042

Rank 5 · TkA03G042240 · 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.

PF25079COB_C40-69 aa

PF04833COBRA_N56-219 aa

PF25079COB_C228-421 aa

PF04833COBRA_N310-328 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G042240	`PF25079`	COB_C	40	69	1.4e-60	205.6
TkA03G042240	`PF04833`	COBRA_N	56	219	5e-68	229.0
TkA03G042240	`PF25079`	COB_C	228	421	1.4e-60	205.6
TkA03G042240	`PF04833`	COBRA_N	310	328	5e-68	229.0

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
`Q94KT8`	Arabidopsis thaliana	sp\|Q94KT8\|COBRA_ARATH Protein COBRA	75.400%	Swiss-Prot	High
`Q9SRT7`	Arabidopsis thaliana	sp\|Q9SRT7\|COBL1_ARATH COBRA-like protein 1	73.400%	Swiss-Prot	High
`Q8L8Q7`	Arabidopsis thaliana	sp\|Q8L8Q7\|COBL2_ARATH COBRA-like protein 2	72.700%	Swiss-Prot	High
`Q60E70`	Oryza sativa subsp. japonica	sp\|Q60E70\|COBL3_ORYSJ COBRA-like protein 3	79.300%	Swiss-Prot	High
`Q6Z4G8`	Oryza sativa subsp. japonica	sp\|Q6Z4G8\|COBL1_ORYSJ COBRA-like protein 1	74.500%	Swiss-Prot	High

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