LXL04_005008 | RubberDandelionOmics

Gene overview

LXL04_005008

Reference: OH-1004 Chr: Chr01 Coordinates: 152873100-152876112 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2154 bp · LXL04_005008|LXL04_005008|OH1004|cDNA

ATGCTGGCTTCTGAAGATACAACAGAGTTTCTTCAGATCCGAAGAAAAAGTGGAGGTGTTGATGATGGACTTGTTCTTGACTCTGGTGAATATTCTATCAAGATATTGACCAGGAATAAAGCACGAAATCGGTTAATTCATGGATTATCCACGGATTCTTCGTATTTATCTGGAGATTTTGAGAGTATGATTACTTTCATGGATTCGAAAGAGAAATTGAAAGAAACTGAGAGATGCTTAGATTCTCAGTTATGGCATGC...

CDS

Download CDS FASTA

2154 bp · LXL04_005008|LXL04_005008|OH1004|CDS

ATGCTGGCTTCTGAAGATACAACAGAGTTTCTTCAGATCCGAAGAAAAAGTGGAGGTGTTGATGATGGACTTGTTCTTGACTCTGGTGAATATTCTATCAAGATATTGACCAGGAATAAAGCACGAAATCGGTTAATTCATGGATTATCCACGGATTCTTCGTATTTATCTGGAGATTTTGAGAGTATGATTACTTTCATGGATTCGAAAGAGAAATTGAAAGAAACTGAGAGATGCTTAGATTCTCAGTTATGGCATGC...

Protein

Download Protein FASTA

717 aa · LXL04_005008|LXL04_005008|OH1004|PROTEIN

MLASEDTTEFLQIRRKSGGVDDGLVLDSGEYSIKILTRNKARNRLIHGLSTDSSYLSGDFESMITFMDSKEKLKETERCLDSQLWHACAGSMIQMPAVNSKVFYFPQGHAEHAAGNVEFRERNSQSRVPAWIPCRVAGVKFMADVETDEVYAKIRLIPVSGSGEFNSFDDEDTSSSNGESSDGQVKPSSFAKTLTQSDANNGGGFSVPRYCAETIFPRLDYSADPPVQTILAKDVHGDTWKFRHIYRGTPRRHLLTTGWS...

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_005008`
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_005008

Location Chr01:152873100-152876112 (-)

Description Similar to ARF18: Auxin response factor 18

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g30080`	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
`At2g28350`	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
`Os06g0685700`	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
`Os10g0479900`	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
`Os02g0628600`	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_005008 · 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:0007389 pattern specification process Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009743 response to carbohydrate Biological Process

GO:0010154 fruit development Biological Process

GO:0031540 regulation of anthocyanin biosynthetic process Biological Process

GO:0048366 leaf development Biological Process

GO:0048441 petal development Biological Process

GO:0048442 sepal development Biological Process

KEGG gene cross-reference

ath:AT2G28350

ath:AT4G30080

dosa:Os02g0628600

dosa:Os06g0685700

dosa:Os10g0479900

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.971

Rank 1 · LXL04_005008 · OH-1004

Cytoplasm0.080

Rank 2 · LXL04_005008 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_005008 · OH-1004

Endoplasmic reticulum0.017

Rank 4 · LXL04_005008 · OH-1004

Plastid0.013

Rank 5 · LXL04_005008 · 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.

PF02362.27B3190-291 aa

PF25313.2BRWD_AD351-453 aa

PF06507.20ARF_AD371-454 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005008	`PF02362.27`	B3	190	291	6.1e-24	84.6
LXL04_005008	`PF25313.2`	BRWD_AD	351	453	6.3e-10	40.0
LXL04_005008	`PF06507.20`	ARF_AD	371	454	2.5e-34	117.7

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
`Q93YR9`	Arabidopsis thaliana	Auxin response factor 16	55.244%	Swiss-Prot	strong database homology
`Q9SKN5`	Arabidopsis thaliana	Auxin response factor 10	54.265%	Swiss-Prot	strong database homology
`Q653H7`	Oryza sativa subsp. japonica	Auxin response factor 18	55.168%	Swiss-Prot	strong database homology
`Q9AV47`	Oryza sativa subsp. japonica	Auxin response factor 22	53.478%	Swiss-Prot	strong database homology
`Q6K223`	Oryza sativa subsp. japonica	Auxin response factor 8	51.700%	Swiss-Prot	strong database homology

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