LXL04_006040 | RubberDandelionOmics

Gene overview

LXL04_006040

Reference: OH-1004 Chr: Chr02 Coordinates: 855173-856161 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

903 bp · LXL04_006040|LXL04_006040|OH1004|cDNA

ATGGATTGGGTTTTCAGATCATCGTCGTCTCCTTGGGACTTCACTGAGCTCGAGAGAGATGAATTTGATCATAATATCGAGGCTTTCTCTATCGACTCGAGCATATTCGGGGAATCAAACTGGCAAAAACATTCAACAATGGCGTCCTCTCCTCctcctcttcctcttcctcttcctcttcctcttcctcttcctcGCTCTCCTGAACCTCTTCTTTCTGGTTCATCGAAGAAGCCACGTGGAGATGTTAACGAGCAGTA...

CDS

Download CDS FASTA

903 bp · LXL04_006040|LXL04_006040|OH1004|CDS

ATGGATTGGGTTTTCAGATCATCGTCGTCTCCTTGGGACTTCACTGAGCTCGAGAGAGATGAATTTGATCATAATATCGAGGCTTTCTCTATCGACTCGAGCATATTCGGGGAATCAAACTGGCAAAAACATTCAACAATGGCGTCCTCTCCTCCTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCGCTCTCCTGAACCTCTTCTTTCTGGTTCATCGAAGAAGCCACGTGGAGATGTTAACGAGCAGTA...

Protein

Download Protein FASTA

300 aa · LXL04_006040|LXL04_006040|OH1004|PROTEIN

MDWVFRSSSSPWDFTELERDEFDHNIEAFSIDSSIFGESNWQKHSTMASSPPPLPLPLPLPLPLPRSPEPLLSGSSKKPRGDVNEQYVSSCLVDGCKADLSSCREYHRRHRVCEAHSKTPVVAIAGEHQRFCQQCSRFHSVVEFDEVKRSCRKRLDGHNRRRRKPRADTMYLNNYQRFFTNHRGTKLLQFGASPAYTWPHEEKSNQQLHKPQLSSSSSSSSLSREKKFPFLLSNYSSSSSSLGQLVEPKHNNDALSLLSN...

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_006040`
TK1151 ID	TkA03G003380
OH-1004 ID	LXL04_006040
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.700
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_006040

Location Chr02:855173-856161 (+)

Description Similar to TGA1: Teosinte glume architecture 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g50670`	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'.	No verified direct reference in this release
`At5g50570`	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0531600`	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' (By similarity).	No verified direct reference in this release
`UniProt: Q2R3Y1`	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006040 · 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:0009620 response to fungus Biological Process

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

GO:0048653 anther development Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0001216 DNA-binding transcription activator activity Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT5G50570

ath:AT5G50670

dosa:Os08g0531600

osa:107276349

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.

Nucleus0.912

Rank 1 · LXL04_006040 · OH-1004

Cytoplasm0.155

Rank 2 · LXL04_006040 · OH-1004

Cell membrane0.038

Rank 3 · LXL04_006040 · OH-1004

Endoplasmic reticulum0.026

Rank 4 · LXL04_006040 · OH-1004

Plastid0.017

Rank 5 · LXL04_006040 · 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.

PF03110.20SBP91-164 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006040	`PF03110.20`	SBP	91	164	1e-30	106.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`P0DI11`	Arabidopsis thaliana	Squamosa promoter-binding-like protein 13B	67.000%	Swiss-Prot	weak database homology
`B9DI20`	Arabidopsis thaliana	Squamosa promoter-binding-like protein 13A	67.000%	Swiss-Prot	weak database homology
`Q6YZE8`	Oryza sativa subsp. japonica	Squamosa promoter-binding-like protein 16	47.486%	Swiss-Prot	moderate database homology
`Q2R3Y1`	Oryza sativa subsp. japonica	Putative squamosa promoter-binding-like protein 19	48.466%	Swiss-Prot	moderate database homology

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