TkA06G392940 | RubberDandelionOmics

Gene overview

TkA06G392940

Reference: TK1151 Chr: Chr06 Coordinates: 97405526-97406336 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

738 bp · TkA06G392940|TK1151|cDNA

ATGGCAAGCTCAGGATCTCCTTGCGATGCTTGCAAGTTCTTGAAGAGGAAATGTGAAACGGGTTGTGTTTTTGCCCCTCATTTCCACCGTGAACAATGGGGTGCCTATTTTCCTGCCGTTCACAGGGTGTTCGGTGCAACAAAAGTCTCCAACCTCCTTACTCACCTCCCTGTTAGTGATCGAGCTGATGCAGCCCTTTCCATTGCCTATGAAGCTCAAGCTAGGGATCAAGATCCCATTTATGGCAGCGTTGGACATAT...

CDS

Download CDS FASTA

738 bp · TkA06G392940|TK1151|CDS

ATGGCAAGCTCAGGATCTCCTTGCGATGCTTGCAAGTTCTTGAAGAGGAAATGTGAAACGGGTTGTGTTTTTGCCCCTCATTTCCACCGTGAACAATGGGGTGCCTATTTTCCTGCCGTTCACAGGGTGTTCGGTGCAACAAAAGTCTCCAACCTCCTTACTCACCTCCCTGTTAGTGATCGAGCTGATGCAGCCCTTTCCATTGCCTATGAAGCTCAAGCTAGGGATCAAGATCCCATTTATGGCAGCGTTGGACATAT...

Protein

Download Protein FASTA

245 aa · TkA06G392940|TK1151|PROTEIN

MASSGSPCDACKFLKRKCETGCVFAPHFHREQWGAYFPAVHRVFGATKVSNLLTHLPVSDRADAALSIAYEAQARDQDPIYGSVGHIVALQQQVISLQSQVAFLKELAAQSLVSGLDGSNYPANVLNGSDGGFPSDTPPPDIQTWFQQPEHPYINMPPFPEINNMNEPMSFNSLGNYENSIVQENDVPFSSFPGSSNLSIDGLDMQVTHNNEWFSQENAEDLHSVVFGAVSFDPEGATFSGNGLF

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	`TkA06G392940`
TK1151 ID	TkA06G392940
OH-1004 ID	LXL04_022728
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	56.800
Protein coverage (%)	TK1151 38.776 / OH-1004 34.296 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 TkA06G392940

Location Chr06:97405526-97406336 (+)

Description Similar to LBD30: LOB domain-containing protein 30

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g58190`	Involved in lateral root formation.	ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis.2007 · DOI: 10.1105/tpc.106.047761
`At2g42440`	LOB domain-containing protein 17.	No verified direct reference in this release
`At2g45420`	Involved in the positive regulation of tracheary element (TE) differentiation.	ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis.2008 · DOI: 10.1105/tpc.108.061796 LBD18/ASL20 regulates lateral root formation in combination with LBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis.2009 · DOI: 10.1104/pp.109.143685 LBD18 acts as a transcriptional activator that directly binds to the EXPANSIN14 promoter in promoting lateral root emergence of Arabidopsis.2013 · DOI: 10.1111/tpj.12013 The AP2/EREBP gene PUCHI Co-Acts with LBD16/ASL18 and LBD18/ASL20 downstream of ARF7 and ARF19 to regulate lateral root development in Arabidopsis.2013 · DOI: 10.1093/pcp/pct081 EXPANSINA17 up-regulated by LBD18/ASL20 promotes lateral root formation during the auxin response.2013 · DOI: 10.1093/pcp/pct105 Lateral Organ Boundaries Domain16 and 18 Act Downstream of the AUXIN1 and LIKE-AUXIN3 Auxin Influx Carriers to Control Lateral Root Development in Arabidopsis.2015 · DOI: 10.1104/pp.15.00578
`At2g42430`	Transcriptional activator.	ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis.2007 · DOI: 10.1105/tpc.106.047761 LBD18/ASL20 regulates lateral root formation in combination with LBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis.2009 · DOI: 10.1104/pp.109.143685 The AP2/EREBP gene PUCHI Co-Acts with LBD16/ASL18 and LBD18/ASL20 downstream of ARF7 and ARF19 to regulate lateral root development in Arabidopsis.2013 · DOI: 10.1093/pcp/pct081 Lateral Organ Boundaries Domain16 and 18 Act Downstream of the AUXIN1 and LIKE-AUXIN3 Auxin Influx Carriers to Control Lateral Root Development in Arabidopsis.2015 · DOI: 10.1104/pp.15.00578

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0149100`	Acts as a positive regulator of adventitious (crown) root formation by promoting its initiation.	Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling.2005 · DOI: 10.1105/tpc.105.030981 ARL1, a LOB-domain protein required for adventitious root formation in rice.2005 · DOI: 10.1111/j.1365-313x.2005.02434.x Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice.2011 · DOI: 10.1186/1471-2164-12-387

Functional annotation source

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Functional annotation source: OH1004 · LXL04_022728 · 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:0009753 response to jasmonic acid Biological Process

GO:0009755 hormone-mediated signaling pathway Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0010089 xylem development Biological Process

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

GO:0010311 lateral root formation Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:1900150 regulation of defense response to fungus Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0000987 cis-regulatory region sequence-specific DNA binding Molecular Function

GO:0001216 DNA-binding transcription activator activity Molecular Function

KEGG gene cross-reference

ath:AT2G42430

ath:AT2G45420

ath:AT3G03760

ath:AT4G00210

ath:AT4G00220

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.

Nucleus0.961

Rank 1 · TkA06G392940 · TK1151

Cytoplasm0.119

Rank 2 · TkA06G392940 · TK1151

Cell membrane0.024

Rank 3 · TkA06G392940 · TK1151

Endoplasmic reticulum0.022

Rank 4 · TkA06G392940 · TK1151

Plastid0.015

Rank 5 · TkA06G392940 · 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.

PF03195LOB7-105 aa

PF00172Zn_clus7-19 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G392940	`PF03195`	LOB	7	105	8.3e-31	107.2
TkA06G392940	`PF00172`	Zn_clus	7	19	0.95	10.3

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
`Q9M2J7`	Arabidopsis thaliana	sp\|Q9M2J7\|LBD29_ARATH LOB domain-containing protein 29	63.400%	Swiss-Prot	Low
`Q9SLB6`	Arabidopsis thaliana	sp\|Q9SLB6\|LBD17_ARATH LOB domain-containing protein 17	59.600%	Swiss-Prot	Low
`O22131`	Arabidopsis thaliana	sp\|O22131\|LBD18_ARATH LOB domain-containing protein 18	63.600%	Swiss-Prot	Low
`Q9SLB7`	Arabidopsis thaliana	sp\|Q9SLB7\|LBD16_ARATH LOB domain-containing protein 16	60.600%	Swiss-Prot	Low
`Q5UG13`	Oryza sativa subsp. japonica	sp\|Q5UG13\|LBD_ORYSJ LOB domain-containing protein CRL1	63.400%	Swiss-Prot	Low

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