LXL04_038847 | RubberDandelionOmics

Gene overview

LXL04_038847

Reference: OH-1004 Chr: Chr09 Coordinates: 51941122-51945170 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1965 bp · LXL04_038847|LXL04_038847|OH1004|cDNA

ATGACACATATTGCTGCTACTCATTTCCCTGGAGGACCTCAATCAGGATCCTCTGGTGATGCCTTGTACAAAGAGTTATGGCATGCCTGTGCTGGCCCCCTTGTCAATGTCCCCTGTGAAGGAGAACGTGTTTATTACTTCCCTCAAGGCCACATGGAACAGCTTGAGGCTTCCATGCATCAAGGATTAGACCAGCAGCTCCCATCATTTAACTTACCAGCCAAAATACTTTGTAAAGTGGTGAATGTTCAGCTTCGGGC...

CDS

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1965 bp · LXL04_038847|LXL04_038847|OH1004|CDS

ATGACACATATTGCTGCTACTCATTTCCCTGGAGGACCTCAATCAGGATCCTCTGGTGATGCCTTGTACAAAGAGTTATGGCATGCCTGTGCTGGCCCCCTTGTCAATGTCCCCTGTGAAGGAGAACGTGTTTATTACTTCCCTCAAGGCCACATGGAACAGCTTGAGGCTTCCATGCATCAAGGATTAGACCAGCAGCTCCCATCATTTAACTTACCAGCCAAAATACTTTGTAAAGTGGTGAATGTTCAGCTTCGGGC...

Protein

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654 aa · LXL04_038847|LXL04_038847|OH1004|PROTEIN

MTHIAATHFPGGPQSGSSGDALYKELWHACAGPLVNVPCEGERVYYFPQGHMEQLEASMHQGLDQQLPSFNLPAKILCKVVNVQLRAEPETDEVYAQITLLPDTNQNEVTSPDPPPPEPPSCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLPPLDMSQQPPWQELVASDLHGNEWHFRHIFRGQPRRHLLTTGWSVFVSAKKLVAGDAFIFLRGENGELRVGVRRVMRLLNNMPSSVISSHSMHLGVLATASHAIATG...

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_038847`
TK1151 ID	TkA04G471510
OH-1004 ID	LXL04_038847
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.700
Protein coverage (%)	TK1151 96.870 / OH-1004 99.388 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_038847

Location Chr09:51941122-51945170 (+)

Description Similar to ARF1: Auxin response factor 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g59750`	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
`At3g61830`	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
`At2g46530`	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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0557200`	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
`Os04g0442000`	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_038847 · 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:0008219 cell death Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0010150 leaf senescence Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G59750

ath:AT2G46530

ath:AT3G61830

dosa:Os02g0557200

dosa:Os04g0442000

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.

Nucleus0.963

Rank 1 · LXL04_038847 · OH-1004

Cytoplasm0.096

Rank 2 · LXL04_038847 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_038847 · OH-1004

Endoplasmic reticulum0.018

Rank 4 · LXL04_038847 · OH-1004

Plastid0.015

Rank 5 · LXL04_038847 · 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.

PF02362.27B3127-227 aa

PF25313.2BRWD_AD252-358 aa

PF06507.20ARF_AD276-358 aa

PF02309.23AUX_IAA529-568 aa

PF02309.23AUX_IAA579-623 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038847	`PF02362.27`	B3	127	227	2.8e-23	82.5
LXL04_038847	`PF25313.2`	BRWD_AD	252	358	9.9e-13	49.2
LXL04_038847	`PF06507.20`	ARF_AD	276	358	6.2e-35	119.7
LXL04_038847	`PF02309.23`	AUX_IAA	529	568	3.5e-14	53.8
LXL04_038847	`PF02309.23`	AUX_IAA	579	623	3.5e-14	53.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8L7G0`	Arabidopsis thaliana	Auxin response factor 1	66.667%	Swiss-Prot	strong database homology
`Q9C5W9`	Arabidopsis thaliana	Auxin response factor 18	53.639%	Swiss-Prot	strong database homology
`Q9ZPY6`	Arabidopsis thaliana	Auxin response factor 11	52.083%	Swiss-Prot	strong database homology
`Q6YVY0`	Oryza sativa subsp. japonica	Auxin response factor 7	63.692%	Swiss-Prot	strong database homology
`Q0JCZ4`	Oryza sativa subsp. japonica	Auxin response factor 9	62.575%	Swiss-Prot	strong database homology

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