LXL04_024778 | RubberDandelionOmics

Gene overview

LXL04_024778

Reference: OH-1004 Chr: Chr05 Coordinates: 98749193-98752375 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2196 bp · LXL04_024778|LXL04_024778|OH1004|cDNA

ATGAAGCTTTCAACATCAGGCGCTGGTCAGCAGCCTCAAGAAGGAGAGAAGAAAAGCTTGAATTCGGAGCTATGGCATGCTTGTGCAGGCCCTCTTGTTTCCCTACCGACAGTAGGGTCTCGAGTAATCTATTTCCCTCAAGGTCATAGTGAGCAGGTGGCCGCTACAACAAATAAAGAAATCGATTCTCACATACCCAACTACCCAAGCCTCCCTCCCCAATTGATCTGCCAACTCCACAATGTCACAATGCATGCAGA...

CDS

Download CDS FASTA

2196 bp · LXL04_024778|LXL04_024778|OH1004|CDS

ATGAAGCTTTCAACATCAGGCGCTGGTCAGCAGCCTCAAGAAGGAGAGAAGAAAAGCTTGAATTCGGAGCTATGGCATGCTTGTGCAGGCCCTCTTGTTTCCCTACCGACAGTAGGGTCTCGAGTAATCTATTTCCCTCAAGGTCATAGTGAGCAGGTGGCCGCTACAACAAATAAAGAAATCGATTCTCACATACCCAACTACCCAAGCCTCCCTCCCCAATTGATCTGCCAACTCCACAATGTCACAATGCATGCAGA...

Protein

Download Protein FASTA

731 aa · LXL04_024778|LXL04_024778|OH1004|PROTEIN

MKLSTSGAGQQPQEGEKKSLNSELWHACAGPLVSLPTVGSRVIYFPQGHSEQVAATTNKEIDSHIPNYPSLPPQLICQLHNVTMHADVETDEVYAQMTLQPLTPQEQKDTFLPVELGIPSRQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDFSQQPPCQELIARDLHDVEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLLLGIRRSSRSQTVMPSSVLSSDSMHIGLLAAAAHAAATN...

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_024778`
TK1151 ID	TkA06G109330
OH-1004 ID	LXL04_024778
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.900
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_024778

Location Chr05:98749193-98752375 (-)

Description Similar to ARF8: Auxin response factor 8

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g37020`	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).	Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation.2005 · DOI: 10.1242/dev.01955 AUXIN RESPONSE FACTOR8 is a negative regulator of fruit initiation in Arabidopsis.2006 · DOI: 10.1105/tpc.105.037192
`At1g30330`	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).	Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation.2005 · DOI: 10.1242/dev.01955

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0677800`	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: A2YG67`	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
`Os04g0671900`	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

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Functional annotation source: OH1004 · LXL04_024778 · 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:0009908 flower development Biological Process

GO:0010154 fruit development Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT1G30330

ath:AT5G37020

dosa:Os06g0677800

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.

Nucleus0.951

Rank 1 · LXL04_024778 · OH-1004

Cytoplasm0.111

Rank 2 · LXL04_024778 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_024778 · OH-1004

Endoplasmic reticulum0.023

Rank 4 · LXL04_024778 · OH-1004

Plastid0.017

Rank 5 · LXL04_024778 · 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.

PF02362.27B3127-228 aa

PF25313.2BRWD_AD250-359 aa

PF06507.20ARF_AD276-359 aa

PF02309.23AUX_IAA608-707 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024778	`PF02362.27`	B3	127	228	1.9e-23	83.0
LXL04_024778	`PF25313.2`	BRWD_AD	250	359	9.9e-10	39.4
LXL04_024778	`PF06507.20`	ARF_AD	276	359	6.1e-34	116.5
LXL04_024778	`PF02309.23`	AUX_IAA	608	707	3.9e-10	40.6

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
`Q9FGV1`	Arabidopsis thaliana	Auxin response factor 8	61.652%	Swiss-Prot	strong database homology
`Q9ZTX8`	Arabidopsis thaliana	Auxin response factor 6	79.193%	Swiss-Prot	moderate database homology
`Q653U3`	Oryza sativa subsp. japonica	Auxin response factor 17	76.050%	Swiss-Prot	moderate database homology
`A2YG67`	Oryza sativa subsp. indica	Auxin response factor 17	76.050%	Swiss-Prot	moderate database homology
`Q0J951`	Oryza sativa subsp. japonica	Auxin response factor 12	76.688%	Swiss-Prot	moderate database homology

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