LXL04_025453 | RubberDandelionOmics

Gene overview

LXL04_025453

Reference: OH-1004 Chr: Chr05 Coordinates: 112034604-112036115 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

691 bp · LXL04_025453|LXL04_025453|OH1004|cDNA

CTACAGAAAAACCAGACACAAGAAGATGGTGAGGGCACCTTGTTTTGACAACCATGGAATTAAGAGAGGTGCATGGAGTGAAGAGGAAGACAATACGTTAAGATTGTACATTCAGAAATACGGTCATCCTAACTGGCGTGAACTTCCCAAGTTGGCTGGTTTATCTAGATGCGGGAAAAGTTGTAGGTTAAGGTGGATCAATTATTTGCGCCCAAACTTAAGGCGTGGGAACTTtacaaaagaagaagaagatgtcATTT...

CDS

Download CDS FASTA

666 bp · LXL04_025453|LXL04_025453|OH1004|CDS

ATGGTGAGGGCACCTTGTTTTGACAACCATGGAATTAAGAGAGGTGCATGGAGTGAAGAGGAAGACAATACGTTAAGATTGTACATTCAGAAATACGGTCATCCTAACTGGCGTGAACTTCCCAAGTTGGCTGGTTTATCTAGATGCGGGAAAAGTTGTAGGTTAAGGTGGATCAATTATTTGCGCCCAAACTTAAGGCGTGGGAACTTTACAAAAGAAGAAGAAGATGTCATTTTAAACTTACATAAAAAGCTTGGGAG...

Protein

Download Protein FASTA

221 aa · LXL04_025453|LXL04_025453|OH1004|PROTEIN

MVRAPCFDNHGIKRGAWSEEEDNTLRLYIQKYGHPNWRELPKLAGLSRCGKSCRLRWINYLRPNLRRGNFTKEEEDVILNLHKKLGSKWSVMAAQLPGRSDNEIKNHWHTHLKNRIRKDKIEQVGSHESTSKGYNPKGCPTERTDLESQEEVGVLIKVLSTGMSSSTTSEQSPNWLSDSGTDARTATAPDVSHRMNIGNDLGTILSVYRNGNKIGIDLVHP

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_025453`
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_025453

Location Chr05:112034604-112036115 (+)

Description Similar to MYB4: Transcription factor MYB4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g31180`	Transcription activator that regulates freezing tolerance by affecting expression of CBF genes.	AtMYB14 Regulates Cold Tolerance in Arabidopsis. 2013 · DOI: 10.1007/s11105-012-0481-z
`At1g79180`	Transcriptional activator that binds DNA to the AC cis-elements 5'-ACCTACC-3', 5'-ACCAACC-3' and 5'-ACCTAAC-3' of promoters and specifically activates lignin biosynthetic genes during secondary wall formation mediated by SND1.	MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis.2009 · DOI: 10.1105/tpc.108.063321
`At3g23250`	Transcription factor involved in cold-regulation of CBF genes and in the development of freezing tolerance.	A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance.2006 · DOI: 10.1074/jbc.m605895200 Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana.2009 · DOI: 10.1016/s1673-8527(09)60003-5

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0517100`	Transcriptional activator involved in cold stress response.	Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants.2004 · DOI: 10.1046/j.1365-313x.2003.01938.x Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development.2010 · DOI: 10.1111/j.1365-3040.2010.02221.x The rice Osmyb4 gene enhances tolerance to frost and improves germination under unfavourable conditions in transgenic barley plants.2012 · DOI: 10.1007/s13353-011-0081-x
`Os02g0624300`	Acts as a negative regulator of cold tolerance.	The OsMYB30 Transcription Factor Suppresses Cold Tolerance by Interacting with a JAZ Protein and Suppressing β-Amylase Expression.2017 · DOI: 10.1104/pp.16.01725

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025453 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009409 response to cold Biological Process

GO:0009411 response to UV Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009809 lignin biosynthetic process Biological Process

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

GO:0050826 response to freezing Biological Process

GO:2000652 regulation of secondary cell wall biogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G79180

ath:AT2G31180

ath:AT3G23250

dosa:Os02g0624300

dosa:Os04g0517100

osa:4330027

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.

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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.

Nucleus0.919

Rank 1 · LXL04_025453 · OH-1004

Cytoplasm0.146

Rank 2 · LXL04_025453 · OH-1004

Cell membrane0.025

Rank 3 · LXL04_025453 · OH-1004

Mitochondrion0.018

Rank 4 · LXL04_025453 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_025453 · 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-binding14-61 aa

PF13921.13Myb_DNA-bind_617-75 aa

PF00249.38Myb_DNA-binding67-112 aa

PF13921.13Myb_DNA-bind_670-122 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025453	`PF00249.38`	Myb_DNA-binding	14	61	4.3e-34	117.1
LXL04_025453	`PF13921.13`	Myb_DNA-bind_6	17	75	7.6e-23	81.2
LXL04_025453	`PF00249.38`	Myb_DNA-binding	67	112	4.3e-34	117.1
LXL04_025453	`PF13921.13`	Myb_DNA-bind_6	70	122	7.6e-23	81.2

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
`Q9SJX8`	Arabidopsis thaliana	Transcription factor MYB14	66.387%	Swiss-Prot	moderate database homology
`Q6R0A6`	Arabidopsis thaliana	Transcription factor MYB63	53.448%	Swiss-Prot	strong database homology
`Q9LTC4`	Arabidopsis thaliana	Transcription factor MYB15	65.517%	Swiss-Prot	moderate database homology
`Q7XBH4`	Oryza sativa subsp. japonica	Transcription factor MYB4	62.406%	Swiss-Prot	moderate database homology
`Q6K1S6`	Oryza sativa subsp. japonica	Transcription factor MYB30	65.517%	Swiss-Prot	moderate database homology

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