LXL04_020508 | RubberDandelionOmics

Gene overview

LXL04_020508

Reference: OH-1004 Chr: Chr04 Coordinates: 84485609-84494744 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2574 bp · LXL04_020508|LXL04_020508|OH1004|cDNA

ATGAAAATTGAGGCAGGAGCTCTTCAATCTCAGGGACGCCGGCTTGTAGGAGACGGAGAAGCTGTGGCGCTTCAAGCTCGGTTGTCGCATGTCGGTGCTTCTAGCTCGGTCATCGCCTATCGGCGCCTCACAGTTTTCTTGCACATATGGTCCTTGGAAAGACAAAGATTACAAAAAGCTTATCAGTTCTTGGGAATGGAATATACAGTCGCCTTGCTCGTTCTTGGCATCGCCATGGGATCAATAGAATATGGAACAAG...

CDS

Download CDS FASTA

2574 bp · LXL04_020508|LXL04_020508|OH1004|CDS

ATGAAAATTGAGGCAGGAGCTCTTCAATCTCAGGGACGCCGGCTTGTAGGAGACGGAGAAGCTGTGGCGCTTCAAGCTCGGTTGTCGCATGTCGGTGCTTCTAGCTCGGTCATCGCCTATCGGCGCCTCACAGTTTTCTTGCACATATGGTCCTTGGAAAGACAAAGATTACAAAAAGCTTATCAGTTCTTGGGAATGGAATATACAGTCGCCTTGCTCGTTCTTGGCATCGCCATGGGATCAATAGAATATGGAACAAG...

Protein

Download Protein FASTA

857 aa · LXL04_020508|LXL04_020508|OH1004|PROTEIN

MKIEAGALQSQGRRLVGDGEAVALQARLSHVGASSSVIAYRRLTVFLHIWSLERQRLQKAYQFLGMEYTVALLVLGIAMGSIEYGTSYRLGKVADGIRNCKLILAALNMNLVHVQGANIDPDLLLATSWALLMRDVKNKIWKKSSSQSTNVLAAATSARDSPPMTVTYRHKGLDREATERMIKELDEDREESQDPEVEFAIAGAVREWKFCWKLFSTELVPVFYKILGMVPVLYKIADMRLRDDLKSNQDAIEPAEGILL...

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_020508`
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_020508

Location Chr04:84485609-84494744 (+)

Description Similar to BIG: Auxin transport protein BIG

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g02260`	Required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development).	BIG: a calossin-like protein required for polar auxin transport in Arabidopsis.2001 · DOI: 10.1101/gad.905201 Mutations in the huge Arabidopsis gene BIG affect a range of hormone and light responses.2003 · DOI: 10.1046/j.1365-313x.2003.01779.x The auxin transport inhibitor response 3 (tir3) allele of BIG and auxin transport inhibitors affect the gibberellin status of Arabidopsis.2005 · DOI: 10.1111/j.1365-313x.2004.02287.x CRM1/BIG-mediated auxin action regulates Arabidopsis inflorescence development.2007 · DOI: 10.1093/pcp/pcm094 Arabidopsis mutants define downstream branches in the phototransduction pathway.1994 · DOI: 10.1101/gad.8.3.339 Reduced naphthylphthalamic acid binding in the tir3 mutant of Arabidopsis is associated with a reduction in polar auxin transport and diverse morphological defects.1997 · DOI: 10.1105/tpc.9.5.745

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0247700`	Required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development) (By similarity).	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_020508 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009620 response to fungus Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009926 auxin polar transport Biological Process

GO:0010311 lateral root formation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0048281 inflorescence morphogenesis Biological Process

GO:0048364 root development Biological Process

GO:0071596 ubiquitin-dependent protein catabolic process via the N-end rule pathway Biological Process

GO:0140455 cytoplasm protein quality control Biological Process

KEGG gene cross-reference

ath:AT3G02260

ddi:DDB_G0283893

dosa:Os09g0247700

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.

Cytoplasm0.476

Rank 1 · LXL04_020508 · OH-1004

Nucleus0.165

Rank 2 · LXL04_020508 · OH-1004

Lysosome / Vacuole0.140

Rank 3 · LXL04_020508 · OH-1004

Endoplasmic reticulum0.130

Rank 4 · LXL04_020508 · OH-1004

Cell membrane0.110

Rank 5 · LXL04_020508 · 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.

PF30837.1UBR4_Ub130-183 aa

PF30838.1UBR4_TPR243-302 aa

PF30837.1UBR4_Ub455-508 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_020508	`PF30837.1`	UBR4_Ub	130	183	7.8e-14	52.2
LXL04_020508	`PF30838.1`	UBR4_TPR	243	302	4.1e-21	76.2
LXL04_020508	`PF30837.1`	UBR4_Ub	455	508	7.8e-14	52.2

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
`Q9SRU2`	Arabidopsis thaliana	Auxin transport protein BIG	35.597%	Swiss-Prot	weak database homology
`B9G2A8`	Oryza sativa subsp. japonica	Auxin transport protein BIG	32.767%	Swiss-Prot	weak database homology

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