LXL04_009931 | RubberDandelionOmics

Gene overview

LXL04_009931

Reference: OH-1004 Chr: Chr02 Coordinates: 136116594-136118113 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

690 bp · LXL04_009931|LXL04_009931|OH1004|cDNA

ATGGATGTGGTGAGTGGAGGTAATGGTCATGACAGCTCAAGTTTAGCTTCTAAACAACGCCTTCGTTGGACTCATGAGCTTCATGAACGATTTGTTGATGCTGTGGCACAATTGGGCGGCCCTGATAGGGCTACCCCAAAAGGTGTGCTGAGAGTGATGGGTGTTCAAGGTCTAACAATTTATCATGTCAAGAGCCACTTGCAGAAATATAGGCTCGCAAAGTATCTTCCAGATTCCTCTTCTGAAGGAAAAGCATTTGA...

CDS

Download CDS FASTA

690 bp · LXL04_009931|LXL04_009931|OH1004|CDS

ATGGATGTGGTGAGTGGAGGTAATGGTCATGACAGCTCAAGTTTAGCTTCTAAACAACGCCTTCGTTGGACTCATGAGCTTCATGAACGATTTGTTGATGCTGTGGCACAATTGGGCGGCCCTGATAGGGCTACCCCAAAAGGTGTGCTGAGAGTGATGGGTGTTCAAGGTCTAACAATTTATCATGTCAAGAGCCACTTGCAGAAATATAGGCTCGCAAAGTATCTTCCAGATTCCTCTTCTGAAGGAAAAGCATTTGA...

Protein

Download Protein FASTA

229 aa · LXL04_009931|LXL04_009931|OH1004|PROTEIN

MDVVSGGNGHDSSSLASKQRLRWTHELHERFVDAVAQLGGPDRATPKGVLRVMGVQGLTIYHVKSHLQKYRLAKYLPDSSSEGKAFDQKESGEMLSSLDGSSGMQITEALKLQMEVQKRLHEQLEVQRQLQLRIEAQGKYLKKIIEEQQKLTGVLSEQDNTCPQPKPPPPVIIENPTPVNTIEPLPLTPEDSGLNRVAKKQRVELTHQILESSLRQQHSVYGMSVNNDG

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_009931`
TK1151 ID	TkA03G483350
OH-1004 ID	LXL04_009931
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.400
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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009931

Location Chr02:136116594-136118113 (+)

Description Similar to PHL7: Myb family transcription factor PHL7

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`UniProt: B8ANX9`	Transcription factor involved in phosphate starvation signaling.	No verified direct reference in this release
`Os03g0329900`	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 Integrative Comparison of the Role of the PHOSPHATE RESPONSE1 Subfamily in Phosphate Signaling and Homeostasis in Rice.2015 · DOI: 10.1104/pp.15.00736

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009931 · 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:0048768 root hair cell tip growth 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

KEGG gene cross-reference

ath:AT2G01060

dosa:Os03g0329900

dosa:Os04g0665600

osa:4337318

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.965

Rank 1 · LXL04_009931 · OH-1004

Cytoplasm0.123

Rank 2 · LXL04_009931 · OH-1004

Cell membrane0.018

Rank 3 · LXL04_009931 · OH-1004

Mitochondrion0.014

Rank 4 · LXL04_009931 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_009931 · OH-1004

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.

PF00249.38Myb_DNA-binding20-71 aa

PF14379.12Myb_CC_LHEQLE104-150 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009931	`PF00249.38`	Myb_DNA-binding	20	71	6.4e-10	39.7
LXL04_009931	`PF14379.12`	Myb_CC_LHEQLE	104	150	1e-23	83.5

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
`Q9SJW0`	Arabidopsis thaliana	Myb family transcription factor PHL7	63.889%	Swiss-Prot	strong database homology
`Q0J995`	Oryza sativa subsp. japonica	Myb family transcription factor RLI1	62.143%	Swiss-Prot	moderate database homology
`A2XYN9`	Oryza sativa subsp. indica	Myb family transcription factor RLI1	62.143%	Swiss-Prot	moderate database homology
`B8ANX9`	Oryza sativa subsp. indica	Protein PHOSPHATE STARVATION RESPONSE 1	65.957%	Swiss-Prot	moderate database homology
`Q10LZ1`	Oryza sativa subsp. japonica	Protein PHOSPHATE STARVATION RESPONSE 1	65.957%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card