LXL04_030652 | RubberDandelionOmics

Gene overview

LXL04_030652

Reference: OH-1004 Chr: Chr06 Coordinates: 120313230-120314018 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

273 bp · LXL04_030652|LXL04_030652|OH1004|cDNA

ATGTCCAGTagaagatcaagaacaagaCAATCAACTTCGAGAATCAGTGACGATCAAATCAACGATCTTGTTTCCAGGTTACAACAACTTCTTCCTGAAATCCGCAATCGCCGCTCTGATAAGGTGTCAGCGTCAAAAGTGCTACAAGAGACATGTAGCTACATCAGAAGCTTGCATCGAGAAGTTGACGATTTAAGTGACCGACTCTCCGAGTTGCTTGAGAACACTGATTCAACTCAGGCTACCATTATTAGGAGTTT...

CDS

Download CDS FASTA

273 bp · LXL04_030652|LXL04_030652|OH1004|CDS

ATGTCCAGTAGAAGATCAAGAACAAGACAATCAACTTCGAGAATCAGTGACGATCAAATCAACGATCTTGTTTCCAGGTTACAACAACTTCTTCCTGAAATCCGCAATCGCCGCTCTGATAAGGTGTCAGCGTCAAAAGTGCTACAAGAGACATGTAGCTACATCAGAAGCTTGCATCGAGAAGTTGACGATTTAAGTGACCGACTCTCCGAGTTGCTTGAGAACACTGATTCAACTCAGGCTACCATTATTAGGAGTTT...

Protein

Download Protein FASTA

90 aa · LXL04_030652|LXL04_030652|OH1004|PROTEIN

MSSRRSRTRQSTSRISDDQINDLVSRLQQLLPEIRNRRSDKVSASKVLQETCSYIRSLHREVDDLSDRLSELLENTDSTQATIIRSLLSQ

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_030652`
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_030652

Location Chr06:120313230-120314018 (+)

Description Similar to PRE4: Transcription factor PRE4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g47710`	Atypical and probable non DNA-binding bHLH transcription factor that integrates multiple signaling pathways to regulate cell elongation and plant development.	The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling.2010 · DOI: 10.1105/tpc.109.065946
`At3g28857`	Atypical and probable non DNA-binding bHLH transcription factor that integrates multiple signaling pathways to regulate cell elongation and plant development.	No verified direct reference in this release
`At1g74500`	Atypical and probable non DNA-binding bHLH transcription factor required for MONOPTEROS-dependent root initiation in embryo.	MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor.2010 · DOI: 10.1038/nature08836 The non-DNA-binding bHLH transcription factor PRE3/bHLH135/ATBS1/TMO7 is involved in the regulation of light signaling pathway in Arabidopsis.2012 · DOI: 10.1111/j.1399-3054.2012.01600.x
`At1g26945`	Atypical and probable non DNA-binding bHLH transcription factor that regulates light-mediated responses in day light conditions by binding and inhibiting the activity of the bHLH transcription factor HFR1, a critical regulator of light signaling and shade avoidance.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os10g0404300`	Atypical and probable non DNA-binding bHLH transcription factor that integrates multiple signaling pathways to regulate cell elongation and plant development.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030652 · 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:0009416 response to light stimulus Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009742 brassinosteroid mediated signaling pathway Biological Process

GO:0010086 embryonic root morphogenesis Biological Process

GO:0040008 regulation of growth Biological Process

GO:0048364 root development Biological Process

GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G26945

ath:AT1G74500

ath:AT3G28857

ath:AT3G47710

osa:107277392

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.

Nucleus0.921

Rank 1 · LXL04_030652 · OH-1004

Cytoplasm0.235

Rank 2 · LXL04_030652 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_030652 · OH-1004

Mitochondrion0.017

Rank 4 · LXL04_030652 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_030652 · 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.

PF23174.1bHLH_ILI16-88 aa

PF00010.32HLH18-59 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030652	`PF23174.1`	bHLH_ILI	16	88	1.4e-32	112.6
LXL04_030652	`PF00010.32`	HLH	18	59	9.3e-07	29.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`F4JCN9`	Arabidopsis thaliana	Transcription factor PRE4	70.652%	Swiss-Prot	strong database homology
`Q9LJX1`	Arabidopsis thaliana	Transcription factor PRE5	70.330%	Swiss-Prot	strong database homology
`Q9CA64`	Arabidopsis thaliana	Transcription factor PRE3	74.026%	Swiss-Prot	strong database homology
`Q8GW32`	Arabidopsis thaliana	Transcription factor PRE6	78.667%	Swiss-Prot	strong database homology
`Q338G6`	Oryza sativa subsp. japonica	Transcription factor ILI7	65.789%	Swiss-Prot	strong database homology

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