LXL04_014733 | RubberDandelionOmics

Gene overview

LXL04_014733

Reference: OH-1004 Chr: Chr03 Coordinates: 55898693-55902770 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1584 bp · LXL04_014733|LXL04_014733|OH1004|cDNA

ATGGAAGAGCCTCAAGAAGTTCATACTGATGAGAATAGAGCTCTTCCTGAAAAGAAACAGAAGAGAATTGTCAAGACACCAGCTCAAGTTGCAGCATTAGAGAACTTCTATAATGAACATAAATATCCCACAGAGGTAATGAAACAAGACCTTGCAGACTCAATCGGCCTAACCGAAAAGCAAGTTTCCGGTTGGTTTTGTCACCGAAGACTCAAAGACAAAAAACCACAAACCGACCATGAAATCCAACCGCCACCTGG...

CDS

Download CDS FASTA

1584 bp · LXL04_014733|LXL04_014733|OH1004|CDS

ATGGAAGAGCCTCAAGAAGTTCATACTGATGAGAATAGAGCTCTTCCTGAAAAGAAACAGAAGAGAATTGTCAAGACACCAGCTCAAGTTGCAGCATTAGAGAACTTCTATAATGAACATAAATATCCCACAGAGGTAATGAAACAAGACCTTGCAGACTCAATCGGCCTAACCGAAAAGCAAGTTTCCGGTTGGTTTTGTCACCGAAGACTCAAAGACAAAAAACCACAAACCGACCATGAAATCCAACCGCCACCTGG...

Protein

Download Protein FASTA

527 aa · LXL04_014733|LXL04_014733|OH1004|PROTEIN

MEEPQEVHTDENRALPEKKQKRIVKTPAQVAALENFYNEHKYPTEVMKQDLADSIGLTEKQVSGWFCHRRLKDKKPQTDHEIQPPPGGKQDRSSGVIQDRGSGLRQDSCGSTKQGDTNKQSDPKEVESRRFTSQNIPPTQIQHHNNLIMHHHHDNNDNHNDDDDDDDDDDDTSSGSSSPLKDGFRPQNVDRVGAIASKYPSHDFKSVRGPSGYLKVKGQVENAAITAVKRQLGRHYREDGPPLGIEFEALPPGAFEIPVK...

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_014733`
TK1151 ID	TkA02G401260
OH-1004 ID	LXL04_014733
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
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_014733

Location Chr03:55898693-55902770 (+)

Description Similar to RLT1: Homeobox-DDT domain protein RLT1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g28420`	Transcriptional regulator required for the maintenance of the plant vegetative phase.	Imitation Switch chromatin remodeling factors and their interacting RINGLET proteins act together in controlling the plant vegetative phase in Arabidopsis.2012 · DOI: 10.1111/j.1365-313x.2012.05074.x
`At5g44180`	Transcriptional regulator required for the maintenance of the plant vegetative phase.	Imitation Switch chromatin remodeling factors and their interacting RINGLET proteins act together in controlling the plant vegetative phase in Arabidopsis.2012 · DOI: 10.1111/j.1365-313x.2012.05074.x Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis.2013 · DOI: 10.1105/tpc.113.112714
`At4g12750`	Transcriptional regulator required for the maintenance of the plant vegetative phase.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_014733 · 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:0009908 flower development Biological Process

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

GO:0045892 negative regulation of DNA-templated transcription Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0005667 transcription regulator complex Cellular Component

GO:0031010 ISWI-type complex Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding Molecular Function

GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific Molecular Function

KEGG gene cross-reference

ath:AT1G28420

ath:AT5G44180

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.

Nucleus0.763

Rank 1 · LXL04_014733 · OH-1004

Cytoplasm0.255

Rank 2 · LXL04_014733 · OH-1004

Cell membrane0.094

Rank 3 · LXL04_014733 · OH-1004

Endoplasmic reticulum0.057

Rank 4 · LXL04_014733 · OH-1004

Golgi apparatus0.018

Rank 5 · LXL04_014733 · 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.

PF00046.36Homeodomain19-75 aa

PF05920.18Homeobox_KN40-70 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014733	`PF00046.36`	Homeodomain	19	75	2.2e-16	60.1
LXL04_014733	`PF05920.18`	Homeobox_KN	40	70	1.4e-06	28.8

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
`F4HY56`	Arabidopsis thaliana	Homeobox-DDT domain protein RLT1	50.877%	Swiss-Prot	weak database homology
`Q9FFH1`	Arabidopsis thaliana	Homeobox-DDT domain protein RLT2	46.774%	Swiss-Prot	weak database homology
`F4JRF5`	Arabidopsis thaliana	Homeobox-DDT domain protein RLT3	54.000%	Swiss-Prot	weak database homology

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