LXL04_017979 | RubberDandelionOmics

Gene overview

LXL04_017979

Reference: OH-1004 Chr: Chr04 Coordinates: 4546402-4548994 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1890 bp · LXL04_017979|LXL04_017979|OH1004|cDNA

ATGATCACTGGAAAGGACATTTACGATGTTCTGGCAGCCATCGTGCCGCTGTACGTCGCCATGATGCTAGCCTACGGCTCCGTGCGGTGGTGGAAAATCTTCACGCCGGATCAGTGCTCCGGCATTAACAGATTCGTCGCCGTGTTCGCCGTTCCGTTGCTTTCTTTCCACTTCATCTCCTCCAACAATCCTTACGAGATGAACTACCATTTCATAGCGGCGGATTCCCTTCAAAAGATCGTAATGCTATCGGCGTTGTT...

CDS

Download CDS FASTA

1890 bp · LXL04_017979|LXL04_017979|OH1004|CDS

ATGATCACTGGAAAGGACATTTACGATGTTCTGGCAGCCATCGTGCCGCTGTACGTCGCCATGATGCTAGCCTACGGCTCCGTGCGGTGGTGGAAAATCTTCACGCCGGATCAGTGCTCCGGCATTAACAGATTCGTCGCCGTGTTCGCCGTTCCGTTGCTTTCTTTCCACTTCATCTCCTCCAACAATCCTTACGAGATGAACTACCATTTCATAGCGGCGGATTCCCTTCAAAAGATCGTAATGCTATCGGCGTTGTT...

Protein

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629 aa · LXL04_017979|LXL04_017979|OH1004|PROTEIN

MITGKDIYDVLAAIVPLYVAMMLAYGSVRWWKIFTPDQCSGINRFVAVFAVPLLSFHFISSNNPYEMNYHFIAADSLQKIVMLSALFIWQWLSKSGSLEWMITLFSLSTLPNTLVMGIPLLKAMYGDFSGSLMVQIVVLQSVIWYTLMLFMFEYRGAKLLITEQFPETAGSITSFHVESDVVSLNGREPLQTDAEIGDDGKLHVVVRRSSTASSRSVISSYNKSHNITGITPRASNLTGVEIYSVQSSRGPTPRASSFNQ...

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_017979`
TK1151 ID	TkA08G035700
OH-1004 ID	LXL04_017979
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.900
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_017979

Location Chr04:4546402-4548994 (-)

Description Similar to PIN2: Auxin efflux carrier component 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g57090`	Acts as a component of the auxin efflux carrier.	No verified direct reference in this release
`At1g23080`	Acts as a component of the auxin efflux carrier.	Efflux-dependent auxin gradients establish the apical-basal axis of Arabidopsis.2003 · DOI: 10.1038/nature02085 Differential auxin-transporting activities of PIN-FORMED proteins in Arabidopsis root hair cells.2010 · DOI: 10.1104/pp.110.156505 Connective auxin transport contributes to strigolactone-mediated shoot branching control independent of the transcription factor BRC1.2019 · DOI: 10.1371/journal.pgen.1008023
`At2g01420`	Acts as a component of the auxin efflux carrier.	Differential auxin-transporting activities of PIN-FORMED proteins in Arabidopsis root hair cells.2010 · DOI: 10.1104/pp.110.156505 Connective auxin transport contributes to strigolactone-mediated shoot branching control independent of the transcription factor BRC1.2019 · DOI: 10.1371/journal.pgen.1008023 Root System Depth in Arabidopsis Is Shaped by EXOCYST70A3 via the Dynamic Modulation of Auxin Transport.2019 · DOI: 10.1016/j.cell.2019.06.021

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0660200`	Acts as a component of the auxin efflux carrier.	Over-expression of OsPIN2 leads to increased tiller numbers, angle and shorter plant height through suppression of OsLAZY1.2012 · DOI: 10.1111/j.1467-7652.2011.00637.x
`Os06g0232300`	May act as a component of the auxin efflux carrier.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017979 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001666 response to hypoxia Biological Process

GO:0009630 gravitropism Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009749 response to glucose Biological Process

GO:0009926 auxin polar transport Biological Process

GO:0009942 longitudinal axis specification Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0010315 auxin export across the plasma membrane Biological Process

GO:0048364 root development Biological Process

KEGG gene cross-reference

ath:AT1G23080

ath:AT2G01420

ath:AT5G57090

dosa:Os06g0232300

dosa:Os06g0660200

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.

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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.

Cell membrane0.830

Rank 1 · LXL04_017979 · OH-1004

Endoplasmic reticulum0.084

Rank 2 · LXL04_017979 · OH-1004

Cytoplasm0.070

Rank 3 · LXL04_017979 · OH-1004

Lysosome / Vacuole0.041

Rank 4 · LXL04_017979 · OH-1004

Nucleus0.033

Rank 5 · LXL04_017979 · 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.

PF03547.24Mem_trans10-624 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017979	`PF03547.24`	Mem_trans	10	624	1.2e-122	409.6

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9LU77`	Arabidopsis thaliana	Auxin efflux carrier component 2	70.499%	Swiss-Prot	strong database homology
`Q940Y5`	Arabidopsis thaliana	Auxin efflux carrier component 7	61.231%	Swiss-Prot	strong database homology
`Q8RWZ6`	Arabidopsis thaliana	Auxin efflux carrier component 4	59.571%	Swiss-Prot	strong database homology
`Q651V6`	Oryza sativa subsp. japonica	Auxin efflux carrier component 2	62.295%	Swiss-Prot	strong database homology
`Q67UL3`	Oryza sativa subsp. japonica	Probable auxin efflux carrier component 1c	59.657%	Swiss-Prot	strong database homology

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