LXL04_007827 | RubberDandelionOmics

Gene overview

LXL04_007827

Reference: OH-1004 Chr: Chr02 Coordinates: 64192814-64204278 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

585 bp · LXL04_007827|LXL04_007827|OH1004|cDNA

atgaaagtgtcattcatcactcactGGTGGAGAAGACGAAGAGGTGTGGATGCGGGAGAGACTGAGTCTTGCGGAAGACTCTCAGTAGTGATAAGTGATGTTGCGCGTTCTGAGAGTCCTGATCTGTTAAAACCACGATCCAACAGTTTCGCTGCTGTAACTCGCaacaaagaagaagaagatgggGGTAGCGACCGGTGGCGACAGTTCATAACCGATGGTTGCGGGAGATTTACTCCAACAAGTGATCATATGGCAAG...

CDS

Download CDS FASTA

585 bp · LXL04_007827|LXL04_007827|OH1004|CDS

ATGAAAGTGTCATTCATCACTCACTGGTGGAGAAGACGAAGAGGTGTGGATGCGGGAGAGACTGAGTCTTGCGGAAGACTCTCAGTAGTGATAAGTGATGTTGCGCGTTCTGAGAGTCCTGATCTGTTAAAACCACGATCCAACAGTTTCGCTGCTGTAACTCGCAACAAAGAAGAAGAAGATGGGGGTAGCGACCGGTGGCGACAGTTCATAACCGATGGTTGCGGGAGATTTACTCCAACAAGTGATCATATGGCAAG...

Protein

Download Protein FASTA

194 aa · LXL04_007827|LXL04_007827|OH1004|PROTEIN

MKVSFITHWWRRRRGVDAGETESCGRLSVVISDVARSESPDLLKPRSNSFAAVTRNKEEEDGGSDRWRQFITDGCGRFTPTSDHMARGKVQMRRIENPVHRQVTFCKRRSGLLKKAKELSILCDAEVGLIIFSSHGKLYELATNGSMQELVEKYMKSTHCSVGEQADEKQFLVSVLLFSRVYYIMFSESDDLLV

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_007827`
TK1151 ID	TkA03G216710
OH-1004 ID	LXL04_007827
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 56.701 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_007827

Location Chr02:64192814-64204278 (-)

Description Similar to MADS26: MADS-box transcription factor 26

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g71692`	Probable transcription activator that regulates root development by controlling cell proliferation in root meristem.	An AGAMOUS-related MADS-box gene, XAL1 (AGL12), regulates root meristem cell proliferation and flowering transition in Arabidopsis.2008 · DOI: 10.1104/pp.107.108647
`At2g14210`	Probable transcription factor.	Nitrate and glutamate sensing by plant roots.2005 · DOI: 10.1042/bst0330283 The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches.2006 · DOI: 10.1073/pnas.0605275103 An Arabidopsis MADS box gene that controls nutrient-induced changes in root architecture.1998 · DOI: 10.1126/science.279.5349.407

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0112700`	Probable transcription factor.	No verified direct reference in this release
`UniProt: A2YQK9`	Probable transcription factor.	No verified direct reference in this release
`Os12g0206800`	Probable transcription factor.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_007827 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0007584 response to nutrient Biological Process

GO:0009908 flower development Biological Process

GO:0010167 response to nitrate Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process

GO:0048364 root development Biological Process

GO:0048527 lateral root development Biological Process

GO:0071249 cellular response to nitrate Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

KEGG gene cross-reference

ath:AT1G71692

ath:AT2G14210

dosa:Os08g0112700

dosa:Os12g0206800

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.

Nucleus0.908

Rank 1 · LXL04_007827 · OH-1004

Cytoplasm0.159

Rank 2 · LXL04_007827 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_007827 · OH-1004

Endoplasmic reticulum0.024

Rank 4 · LXL04_007827 · OH-1004

Mitochondrion0.017

Rank 5 · LXL04_007827 · 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.

PF00319.24SRF-TF94-140 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007827	`PF00319.24`	SRF-TF	94	140	2.4e-25	88.4

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
`Q38841`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL12	74.324%	Swiss-Prot	weak database homology
`Q9SI38`	Arabidopsis thaliana	MADS-box transcription factor ANR1	71.429%	Swiss-Prot	weak database homology
`Q0J8G8`	Oryza sativa subsp. japonica	MADS-box transcription factor 26	72.289%	Swiss-Prot	weak database homology
`A2YQK9`	Oryza sativa subsp. indica	MADS-box transcription factor 26	72.289%	Swiss-Prot	weak database homology
`Q2QW55`	Oryza sativa subsp. japonica	MADS-box transcription factor 33	82.857%	Swiss-Prot	weak database homology

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