TkA06G402940 | RubberDandelionOmics

Gene overview

TkA06G402940

Reference: TK1151 Chr: Chr06 Coordinates: 99743989-99745608 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1494 bp · TkA06G402940|TK1151|cDNA

ATAGATTAATAGCATATTTGTGAACTCCACTTCTTTTGTCCAACCACCATCCATCATCTCCATATGCTTACTGTCAACCTCTTTTCATTTCCACAAAAGCCCTAATTTCAAACCTGTCTTTTGGACAAATTCTTCATCACTTATCCAGACCCTTCCTCTTTCTCTCTCTAGTACTTGCAGTTGTATACCCTTTTCTAGGTAAAAAGAATGGGAAGTAACTGCTCATTTCTGCCAATCTTTCTTTCAACACTTTCTTAATG...

CDS

Download CDS FASTA

600 bp · TkA06G402940|TK1151|CDS

ATGGAAAAGTATCACTCTTTCACCATGGATGTACCTCAAATACAAGAAGATGACTCGATTATCACCACGAACTTTAACGCAAATATGTTGAGCCCAACGTTCTCTTCATCCTCGTCGTCGTCGTCTTCTTCTCCGGCCACTACTCTCAGCCGCTACGAGAACCAAAAACGCCGCGACTGGAACACCTTTGGACAGTACCTACGCAACCACCGTCCGCCGTTAGCTCTTTCCCGGTGCAGCGGTGCACACGTTCTCGAATT...

Protein

Download Protein FASTA

199 aa · TkA06G402940|TK1151|PROTEIN

MEKYHSFTMDVPQIQEDDSIITTNFNANMLSPTFSSSSSSSSSSPATTLSRYENQKRRDWNTFGQYLRNHRPPLALSRCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLRAAYEENGGKPETNPFGARAVRLYLREVRDSQAKARGISYEKKKRKRPPQLPPQQTPLQPPAPLS

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	`TkA06G402940`
TK1151 ID	TkA06G402940
OH-1004 ID	LXL04_023097
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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 TkA06G402940

Location Chr06:99743989-99745608 (+)

Description Similar to LSH6: Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g23290`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light (By similarity).	CUP-SHAPED COTYLEDON1 transcription factor activates the expression of LSH4 and LSH3, two members of the ALOG gene family, in shoot organ boundary cells.2011 · DOI: 10.1111/j.1365-313x.2011.04571.x
`At2g31160`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light (By similarity).	Organ boundary1 defines a gene expressed at the junction between the shoot apical meristem and lateral organs.2011 · DOI: 10.1073/pnas.1018542108
`At1g07090`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2XAV5`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`Os02g0811000`	Transcription factor required for lateral development of the lemma and palea.	TH1, a DUF640 domain-like gene controls lemma and palea development in rice.2012 · DOI: 10.1007/s11103-011-9868-8 Beak-shaped grain 1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice.2013 · DOI: 10.1007/s11427-013-4449-5 The pleiotropic ABNORMAL FLOWER AND DWARF1 affects plant height, floral development and grain yield in rice.2016 · DOI: 10.1111/jipb.12441

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_023097 · 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:0009299 mRNA transcription Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0010199 organ boundary specification between lateral organs and the meristem Biological Process

GO:0010492 maintenance of shoot apical meristem identity Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0048441 petal development Biological Process

GO:0048834 specification of petal number Biological Process

GO:0080050 regulation of seed development Biological Process

GO:0090698 post-embryonic plant morphogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G07090

ath:AT2G31160

ath:AT3G23290

dosa:Os02g0811000

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.

Nucleus0.868

Rank 1 · TkA06G402940 · TK1151

Cytoplasm0.249

Rank 2 · TkA06G402940 · TK1151

Mitochondrion0.043

Rank 3 · TkA06G402940 · TK1151

Cell membrane0.018

Rank 4 · TkA06G402940 · TK1151

Endoplasmic reticulum0.014

Rank 5 · TkA06G402940 · 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.

PF30938ATR719-49 aa

PF04852ALOG_dom39-164 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G402940	`PF30938`	ATR7	19	49	2.4	8.4
TkA06G402940	`PF04852`	ALOG_dom	39	164	1.6e-67	226.1

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
`Q9LW68`	Arabidopsis thaliana	sp\|Q9LW68\|LSH4_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4	93.800%	Swiss-Prot	Medium
`O82268`	Arabidopsis thaliana	sp\|O82268\|LSH3_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 3	72.300%	Swiss-Prot	High
`Q9LMK2`	Arabidopsis thaliana	sp\|Q9LMK2\|LSH6_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6	79.900%	Swiss-Prot	Medium
`A2XAV5`	Oryza sativa subsp. indica	sp\|A2XAV5\|G1L6_ORYSI Protein G1-like6	89.900%	Swiss-Prot	Medium
`Q6K5X1`	Oryza sativa subsp. japonica	sp\|Q6K5X1\|G1L6_ORYSJ Protein G1-like6	89.900%	Swiss-Prot	Medium

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