LXL04_000956 | RubberDandelionOmics

Gene overview

LXL04_000956

Reference: OH-1004 Chr: Chr01 Coordinates: 17390129-17393745 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1764 bp · LXL04_000956|LXL04_000956|OH1004|cDNA

ATGGGGGTTAGTGCATTACACCAAGCACTCAAGAATCTCTGTCTTAACACCGACTGGAATTATGCCGTCTTTTGGAAACTCAATCCAGGAGCTCGAATGATGTTGACTTGCGAAGATGCTTATTATGACAAAAATGATCCTTCAGGGGGCATAAAACGGTTCGATAAAATGATGGGAAATTTGCCTGAACAAGATCTTCTTGACCTAGCAGTGGCAAATATGTCTTTTCACAGATATGCTCTCGGGGAAGGAGTTGTTGG...

CDS

Download CDS FASTA

1764 bp · LXL04_000956|LXL04_000956|OH1004|CDS

ATGGGGGTTAGTGCATTACACCAAGCACTCAAGAATCTCTGTCTTAACACCGACTGGAATTATGCCGTCTTTTGGAAACTCAATCCAGGAGCTCGAATGATGTTGACTTGCGAAGATGCTTATTATGACAAAAATGATCCTTCAGGGGGCATAAAACGGTTCGATAAAATGATGGGAAATTTGCCTGAACAAGATCTTCTTGACCTAGCAGTGGCAAATATGTCTTTTCACAGATATGCTCTCGGGGAAGGAGTTGTTGG...

Protein

Download Protein FASTA

587 aa · LXL04_000956|LXL04_000956|OH1004|PROTEIN

MGVSALHQALKNLCLNTDWNYAVFWKLNPGARMMLTCEDAYYDKNDPSGGIKRFDKMMGNLPEQDLLDLAVANMSFHRYALGEGVVGRVAVADKHLWICGDQLVNDPRLSFEDYDGWRTQFAAGIRTILVVGVIPHGVIQLGSLKNIPEDLKTVNDIRETFLELQTSLTGYIPTITNSYTDTITSINFGIDNRNPESQTPIPSNFQIETNTMENTSFNFPAGCELYEALGPAFYAQNETYNGQTVNEIPGMNNSGLLTPN...

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_000956`
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_000956

Location Chr01:17390129-17393745 (+)

Description Similar to EMB1444: Transcription factor EMB1444

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g06150`	Transcription factor that may regulate root development.	No verified direct reference in this release
`At2g31280`	Transcription factor that may regulate root development.	No verified direct reference in this release
`At1g64625`	Transcription factor that may regulate root development.	No verified direct reference in this release
`At2g27230`	Transcription activator that regulates root development; promotes the production of stele cells in roots.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os11g0446000`	Involved in the repression of jasmonate (JA)-induced genes.	RICE SALT SENSITIVE3 forms a ternary complex with JAZ and class-C bHLH factors and regulates jasmonate-induced gene expression and root cell elongation.2013 · DOI: 10.1105/tpc.113.112052

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000956 · 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:0007140 male meiotic nuclear division Biological Process

GO:0010089 xylem development Biological Process

GO:0048316 seed development Biological Process

GO:0048364 root development Biological Process

GO:0051321 meiotic cell cycle Biological Process

GO:0071365 cellular response to auxin stimulus Biological Process

GO:0090058 metaxylem development Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT1G06150

ath:AT1G64625

ath:AT2G31280

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.

Nucleus0.897

Rank 1 · LXL04_000956 · OH-1004

Cytoplasm0.155

Rank 2 · LXL04_000956 · OH-1004

Cell membrane0.047

Rank 3 · LXL04_000956 · OH-1004

Endoplasmic reticulum0.031

Rank 4 · LXL04_000956 · OH-1004

Plastid0.019

Rank 5 · LXL04_000956 · 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.

PF14215.13bHLH-MYC_N6-161 aa

PF23176.1bHLH_LHW351-412 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000956	`PF14215.13`	bHLH-MYC_N	6	161	1.3e-31	111.0
LXL04_000956	`PF23176.1`	bHLH_LHW	351	412	1.6e-37	128.0

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
`P0C7P8`	Arabidopsis thaliana	Transcription factor EMB1444	46.348%	Swiss-Prot	moderate database homology
`Q58G01`	Arabidopsis thaliana	Transcription factor bHLH155	46.884%	Swiss-Prot	moderate database homology
`Q7XJU0`	Arabidopsis thaliana	Transcription factor bHLH157	31.915%	Swiss-Prot	moderate database homology
`Q9XIN0`	Arabidopsis thaliana	Transcription factor LHW	44.484%	Swiss-Prot	weak database homology
`K4PW38`	Oryza sativa subsp. japonica	Protein RICE SALT SENSITIVE 3	30.453%	Swiss-Prot	weak database homology

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