LXL04_015063 | RubberDandelionOmics

Gene overview

LXL04_015063

Reference: OH-1004 Chr: Chr03 Coordinates: 62835615-62840721 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2658 bp · LXL04_015063|LXL04_015063|OH1004|cDNA

ATGACCACTTTCACAGAAAGTTGTAGTATGGCCGCCATTGAAGAGAAGCTCAATTCATCAGGTGTGAACAGTGGGGCACACAGCTTACTTGAAGAGATGAAATTGTTGAAGGAAATGCAGGACCATTCTGTGCTAAAGAAGCCAATAAATTCGGAGCTGTGGCATGCATGTGCTGGGCCATTGGTGTCTCTTCCACAAGTTGGAAGCCTTGTTTATTACTTCCCACAAGGACATAGCGAACAGGTTGCAGTTTCGACCAA...

CDS

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2658 bp · LXL04_015063|LXL04_015063|OH1004|CDS

ATGACCACTTTCACAGAAAGTTGTAGTATGGCCGCCATTGAAGAGAAGCTCAATTCATCAGGTGTGAACAGTGGGGCACACAGCTTACTTGAAGAGATGAAATTGTTGAAGGAAATGCAGGACCATTCTGTGCTAAAGAAGCCAATAAATTCGGAGCTGTGGCATGCATGTGCTGGGCCATTGGTGTCTCTTCCACAAGTTGGAAGCCTTGTTTATTACTTCCCACAAGGACATAGCGAACAGGTTGCAGTTTCGACCAA...

Protein

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885 aa · LXL04_015063|LXL04_015063|OH1004|PROTEIN

MTTFTESCSMAAIEEKLNSSGVNSGAHSLLEEMKLLKEMQDHSVLKKPINSELWHACAGPLVSLPQVGSLVYYFPQGHSEQVAVSTNRTATSQVPNYPNLPSQLLCQVLNATLHADKDTDEIYAQMSLRPVNSEKDVLPIPDFGMKPSRHPTEFFCKTLTPSDTSTHGGFSVPRRAAEKLFPQLDFSMQPPTQELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSMFVGAKRLKAGDAVLFIRDEKSQLLLGVRRANRQQ...

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_015063`
TK1151 ID	TkA02G371100
OH-1004 ID	LXL04_015063
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.200
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_015063

Location Chr03:62835615-62840721 (-)

Description Similar to ARF5: Auxin response factor 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g19850`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4.2004 · DOI: 10.1242/dev.00925 AMP1 and MP antagonistically regulate embryo and meristem development in Arabidopsis.2007 · DOI: 10.1242/dev.006759

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0664400`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release
`UniProt: Q01K26`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release
`Os06g0702600`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release
`Os12g0613700`	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_015063 · 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:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009908 flower development Biological Process

GO:0009942 longitudinal axis specification Biological Process

GO:0010051 xylem and phloem pattern formation Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0048364 root development Biological Process

GO:0048507 meristem development Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G19850

dosa:Os04g0664400

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.

Nucleus0.950

Rank 1 · LXL04_015063 · OH-1004

Cytoplasm0.110

Rank 2 · LXL04_015063 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_015063 · OH-1004

Endoplasmic reticulum0.022

Rank 4 · LXL04_015063 · OH-1004

Plastid0.018

Rank 5 · LXL04_015063 · 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.

PF02362.27B3155-256 aa

PF25313.2BRWD_AD284-387 aa

PF06507.20ARF_AD304-386 aa

PF02309.23AUX_IAA770-848 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015063	`PF02362.27`	B3	155	256	1.7e-23	83.2
LXL04_015063	`PF25313.2`	BRWD_AD	284	387	4.7e-09	37.2
LXL04_015063	`PF06507.20`	ARF_AD	304	386	4e-31	107.4
LXL04_015063	`PF02309.23`	AUX_IAA	770	848	2.6e-11	44.4

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
`P93024`	Arabidopsis thaliana	Auxin response factor 5	55.731%	Swiss-Prot	strong database homology
`Q8S983`	Oryza sativa subsp. japonica	Auxin response factor 11	73.858%	Swiss-Prot	weak database homology
`Q01K26`	Oryza sativa subsp. indica	Auxin response factor 11	73.858%	Swiss-Prot	weak database homology
`Q0D9R7`	Oryza sativa subsp. japonica	Auxin response factor 19	71.893%	Swiss-Prot	weak database homology
`Q2QM84`	Oryza sativa subsp. japonica	Auxin response factor 25	66.575%	Swiss-Prot	weak database homology

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