LXL04_000409 | RubberDandelionOmics

Gene overview

LXL04_000409

Reference: OH-1004 Chr: Chr01 Coordinates: 7642253-7646829 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1464 bp · LXL04_000409|LXL04_000409|OH1004|cDNA

ATGAATAGCACTTTAAAGATTGGTTGCAACCACGAAACGGTTTACAATCTGAAAGCACATCAACAACCATGGCAAGTTGGAATTACCATTTTGCCATCGGAAATCGAGGGAAGAGGTGTAATCAACCAGCAAGAAGAAcgacaacaacaacagcaacagaTGATAAGTTATAGACAAGAACTTCCATCGTGTAGTAAGACGATTATGGAACAGATTGGGTCACCATCTTCTGCAGTTTTCGCGACTGAAAAATACCTGGG...

CDS

Download CDS FASTA

1464 bp · LXL04_000409|LXL04_000409|OH1004|CDS

ATGAATAGCACTTTAAAGATTGGTTGCAACCACGAAACGGTTTACAATCTGAAAGCACATCAACAACCATGGCAAGTTGGAATTACCATTTTGCCATCGGAAATCGAGGGAAGAGGTGTAATCAACCAGCAAGAAGAACGACAACAACAACAGCAACAGATGATAAGTTATAGACAAGAACTTCCATCGTGTAGTAAGACGATTATGGAACAGATTGGGTCACCATCTTCTGCAGTTTTCGCGACTGAAAAATACCTGGG...

Protein

Download Protein FASTA

487 aa · LXL04_000409|LXL04_000409|OH1004|PROTEIN

MNSTLKIGCNHETVYNLKAHQQPWQVGITILPSEIEGRGVINQQEERQQQQQQMISYRQELPSCSKTIMEQIGSPSSAVFATEKYLGFSQNGVRRSVNDETDVSSVPQMRFDHHFMQPSNNGVFSSYERPFKMRCGNQSERDQIRELKRKLLDESDNSDWRQSQPSICYDGNQDLGGQFGHSMHNGRPPSGQLSGNCTNSVNVMPSKTRIRWTQDLHDRFVECVSCLGGAEKATPKAILKLMDSEGLTIFHVKSHLQKYR...

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	`LXL04_000409`
TK1151 ID	TkA01G613540
OH-1004 ID	LXL04_000409
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	99.500
Protein coverage (%)	TK1151 99.740 / OH-1004 78.850 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_000409

Location Chr01:7642253-7646829 (-)

Description Similar to PHL5: Myb family transcription factor PHL5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g06800`	Myb family transcription factor PHL5.	No verified direct reference in this release
`At2g01060`	Myb family transcription factor PHL7.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0665600`	Transcription factor binding to specific DNA sequences of target genes promoters, such as the motif R1BS 5'-NAKATNCN-3' and the motif P1BS 5'-GNATATNC-3' to trigger their expression.	An SPX-RLI1 Module Regulates Leaf Inclination in Response to Phosphate Availability in Rice.2018 · DOI: 10.1105/tpc.17.00738 Modulation of nitrate-induced phosphate response by the MYB transcription factor RLI1/HINGE1 in the nucleus.2021 · DOI: 10.1016/j.molp.2020.12.005
`UniProt: A2XYN9`	Transcription factor binding to specific DNA sequences of target genes promoters, such as the motif R1BS 5'-NAKATNCN-3' and the motif P1BS 5'-GNATATNC-3' to trigger their expression (By similarity).	No verified direct reference in this release
`Os07g0438800`	Transcription factor involved in phosphate starvation signaling.	OsPHR2 is involved in phosphate-starvation signaling and excessive phosphate accumulation in shoots of plants.2008 · DOI: 10.1104/pp.107.111443 Role of OsPHR2 on phosphorus homeostasis and root hairs development in rice (Oryza sativa L.).2008 · DOI: 10.4161/psb.3.9.5781 OsSPX1 suppresses the function of OsPHR2 in the regulation of expression of OsPT2 and phosphate homeostasis in shoots of rice.2010 · DOI: 10.1111/j.1365-313x.2010.04170.x SPX4 Negatively Regulates Phosphate Signaling and Homeostasis through Its Interaction with PHR2 in Rice.2014 · DOI: 10.1105/tpc.114.123208 Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner.2014 · DOI: 10.1073/pnas.1404680111 Genetic manipulation of a high-affinity PHR1 target cis-element to improve phosphorous uptake in Oryza sativa L.2015 · DOI: 10.1007/s11103-015-0289-y Integrative Comparison of the Role of the PHOSPHATE RESPONSE1 Subfamily in Phosphate Signaling and Homeostasis in Rice.2015 · DOI: 10.1104/pp.15.00736 Modulation of nitrate-induced phosphate response by the MYB transcription factor RLI1/HINGE1 in the nucleus.2021 · DOI: 10.1016/j.molp.2020.12.005

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000409 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009742 brassinosteroid mediated signaling pathway Biological Process

GO:0010167 response to nitrate Biological Process

GO:0010966 regulation of phosphate transport Biological Process

GO:0016036 cellular response to phosphate starvation Biological Process

GO:0016132 brassinosteroid biosynthetic process Biological Process

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

GO:0051511 negative regulation of unidimensional cell growth Biological Process

GO:2000024 regulation of leaf development Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT5G06800

dosa:Os04g0665600

osa:4337318

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 · LXL04_000409 · OH-1004

Cytoplasm0.122

Rank 2 · LXL04_000409 · OH-1004

Cell membrane0.018

Rank 3 · LXL04_000409 · OH-1004

Mitochondrion0.012

Rank 4 · LXL04_000409 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_000409 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00249.38Myb_DNA-binding211-260 aa

PF14379.12Myb_CC_LHEQLE291-337 aa

PF14379.12Myb_CC_LHEQLE405-450 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000409	`PF00249.38`	Myb_DNA-binding	211	260	2.7e-06	28.1
LXL04_000409	`PF14379.12`	Myb_CC_LHEQLE	291	337	2.8e-31	107.7
LXL04_000409	`PF14379.12`	Myb_CC_LHEQLE	405	450	2.8e-31	107.7

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
`Q0WVU3`	Arabidopsis thaliana	Myb family transcription factor PHL5	65.605%	Swiss-Prot	weak database homology
`Q9SJW0`	Arabidopsis thaliana	Myb family transcription factor PHL7	52.318%	Swiss-Prot	weak database homology
`Q0J995`	Oryza sativa subsp. japonica	Myb family transcription factor RLI1	61.538%	Swiss-Prot	weak database homology
`A2XYN9`	Oryza sativa subsp. indica	Myb family transcription factor RLI1	61.538%	Swiss-Prot	weak database homology
`Q6Z156`	Oryza sativa subsp. japonica	Protein PHOSPHATE STARVATION RESPONSE 2	49.390%	Swiss-Prot	weak database homology

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