LXL04_003062 | RubberDandelionOmics

Gene overview

LXL04_003062

Reference: OH-1004 Chr: Chr01 Coordinates: 66114829-66120904 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3066 bp · LXL04_003062|LXL04_003062|OH1004|cDNA

ATGAAGACACCGGGAAACAGTTCTGGATCCACTTTAACAACGGTGAATCCCGGCGAAGGTGGAGAGAAGAACCGGATAATAAATCCGGAGCTATGGCAAGCCTGTGCCGGACCTCTGGTCAACTTACCGGCGGCTGGGACCCACGTCGTCTACTTCCCACAAGGCCACAGCGAGCAGGTTGCTGCGTCTATGAAGAAAGATGTGGATGCTCAAATTCCAAACTATCCCAATCTTCAGTCAAAATTGTTATGCATCCTTCA...

CDS

Download CDS FASTA

3066 bp · LXL04_003062|LXL04_003062|OH1004|CDS

ATGAAGACACCGGGAAACAGTTCTGGATCCACTTTAACAACGGTGAATCCCGGCGAAGGTGGAGAGAAGAACCGGATAATAAATCCGGAGCTATGGCAAGCCTGTGCCGGACCTCTGGTCAACTTACCGGCGGCTGGGACCCACGTCGTCTACTTCCCACAAGGCCACAGCGAGCAGGTTGCTGCGTCTATGAAGAAAGATGTGGATGCTCAAATTCCAAACTATCCCAATCTTCAGTCAAAATTGTTATGCATCCTTCA...

Protein

Download Protein FASTA

1021 aa · LXL04_003062|LXL04_003062|OH1004|PROTEIN

MKTPGNSSGSTLTTVNPGEGGEKNRIINPELWQACAGPLVNLPAAGTHVVYFPQGHSEQVAASMKKDVDAQIPNYPNLQSKLLCILHNITLHADTETDEVYAQMTLQPVPSFDKEALLRSDLLMKAHKPQTEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLDFSMQPPAQELVARDLHDNVWTFRHIYRGQPKRHLLTTGWSLFVSGKRLFAGDSVLFIRDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAA...

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_003062`
TK1151 ID	TkA01G398330
OH-1004 ID	LXL04_003062
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	98.700
Protein coverage (%)	TK1151 53.726 / OH-1004 43.683 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_003062

Location Chr01:66114829-66120904 (-)

Description Similar to ARF19: Auxin response factor 19

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g19220`	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).	A role for auxin response factor 19 in auxin and ethylene signaling in Arabidopsis.2006 · DOI: 10.1104/pp.105.070987 ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis.2007 · DOI: 10.1105/tpc.106.047761 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation.2017 · DOI: 10.1126/scisignal.aan0316
`At5g20730`	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 A gradient of auxin and auxin-dependent transcription precedes tropic growth responses.2006 · DOI: 10.1073/pnas.0507127103 A role for auxin response factor 19 in auxin and ethylene signaling in Arabidopsis.2006 · DOI: 10.1104/pp.105.070987 ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis.2007 · DOI: 10.1105/tpc.106.047761 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation.2017 · DOI: 10.1126/scisignal.aan0316

Rice

Reference gene ID	Possible function	Papers / DOI
`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
`Os02g0141100`	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
`Os08g0520500`	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_003062 · 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:0009734 auxin-activated signaling pathway Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

KEGG gene cross-reference

dosa:Os02g0141100

dosa:Os06g0702600

dosa:Os08g0520500

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.

Nucleus0.952

Rank 1 · LXL04_003062 · OH-1004

Cytoplasm0.097

Rank 2 · LXL04_003062 · OH-1004

Cell membrane0.035

Rank 3 · LXL04_003062 · OH-1004

Endoplasmic reticulum0.027

Rank 4 · LXL04_003062 · OH-1004

Plastid0.017

Rank 5 · LXL04_003062 · 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.

PF02362.27B3134-236 aa

PF06507.20ARF_AD283-343 aa

PF02309.23AUX_IAA908-993 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003062	`PF02362.27`	B3	134	236	7.3e-22	77.9
LXL04_003062	`PF06507.20`	ARF_AD	283	343	8.9e-22	77.5
LXL04_003062	`PF02309.23`	AUX_IAA	908	993	2.1e-07	31.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8RYC8`	Arabidopsis thaliana	Auxin response factor 19	63.924%	Swiss-Prot	weak database homology
`P93022`	Arabidopsis thaliana	Auxin response factor 7	59.546%	Swiss-Prot	weak database homology
`Q0D9R7`	Oryza sativa subsp. japonica	Auxin response factor 19	68.619%	Swiss-Prot	weak database homology
`Q6Z2W3`	Oryza sativa subsp. japonica	Auxin response factor 5	58.974%	Swiss-Prot	moderate database homology
`Q6YZW0`	Oryza sativa subsp. japonica	Auxin response factor 21	61.394%	Swiss-Prot	weak database homology

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