LXL04_038005 | RubberDandelionOmics

Gene overview

LXL04_038005

Reference: OH-1004 Chr: Chr09 Coordinates: 28004156-28007275 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1956 bp · LXL04_038005|LXL04_038005|OH1004|cDNA

ATGAATGCTTCTGGTTCCACTTTTACTTCCATGCTTTCAAGTCCTTTGTCTTCTCCAAATGTCACCGCCCTTCTCAAAATCAAGATCATTTCATGGAGTCAAGAAACAGGCTTACCCGCTTCGGTTTGTGTCCATGTTTCTGACAGAATCTTCAATCTTCATAAGTATCCTTTATGCTCCAAAAGCGGATTCTTTAACAGAAAACTAACGGAATCAAACATCGTTAACTTACCCGACAATTTCCCTGGTGGGCCCGAGAC...

CDS

Download CDS FASTA

1956 bp · LXL04_038005|LXL04_038005|OH1004|CDS

ATGAATGCTTCTGGTTCCACTTTTACTTCCATGCTTTCAAGTCCTTTGTCTTCTCCAAATGTCACCGCCCTTCTCAAAATCAAGATCATTTCATGGAGTCAAGAAACAGGCTTACCCGCTTCGGTTTGTGTCCATGTTTCTGACAGAATCTTCAATCTTCATAAGTATCCTTTATGCTCCAAAAGCGGATTCTTTAACAGAAAACTAACGGAATCAAACATCGTTAACTTACCCGACAATTTCCCTGGTGGGCCCGAGAC...

Protein

Download Protein FASTA

651 aa · LXL04_038005|LXL04_038005|OH1004|PROTEIN

MNASGSTFTSMLSSPLSSPNVTALLKIKIISWSQETGLPASVCVHVSDRIFNLHKYPLCSKSGFFNRKLTESNIVNLPDNFPGGPETFEMISLFIYGSSTLVDPFNVAALRCASEYLEMTEEYTSGNLCERFDIYLNQVVLQSWEDTLIVLQQCQRQNLVPWAEELLIVSRCIESLAFMACMEILDPERRRDQPVVTLEAISFQKWSSEMVQEILTQDVWIKDLIALPFGYFKRVISSLRRQGMKEKYVTPIVLFYANLV...

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_038005`
TK1151 ID	TkA04G373940
OH-1004 ID	LXL04_038005
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.200
Protein coverage (%)	TK1151 100.000 / OH-1004 98.464 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_038005

Location Chr09:28004156-28007275 (+)

Description Similar to At5g48130: BTB/POZ domain-containing protein At5g48130

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g48130`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g13600`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g67385`	Acts as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (Probable).	No verified direct reference in this release
`At1g30440`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g67440`	May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	NPY genes and AGC kinases define two key steps in auxin-mediated organogenesis in Arabidopsis.2008 · DOI: 10.1073/pnas.0809761106 NPY genes play an essential role in root gravitropic responses in Arabidopsis.2011 · DOI: 10.1093/mp/ssq052

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038005 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009904 chloroplast accumulation movement Biological Process

GO:0009908 flower development Biological Process

GO:0009911 positive regulation of flower development Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0071365 cellular response to auxin stimulus Biological Process

GO:1901703 protein localization involved in auxin polar transport Biological Process

GO:2000012 regulation of auxin polar transport Biological Process

GO:0005634 nucleus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT1G30440

ath:AT5G13600

ath:AT5G48130

ath:AT5G67385

ath:AT5G67440

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.

Nucleus0.428

Rank 1 · LXL04_038005 · OH-1004

Cytoplasm0.421

Rank 2 · LXL04_038005 · OH-1004

Cell membrane0.171

Rank 3 · LXL04_038005 · OH-1004

Endoplasmic reticulum0.056

Rank 4 · LXL04_038005 · OH-1004

Golgi apparatus0.047

Rank 5 · LXL04_038005 · 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.

PF03000.20NPH3218-447 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038005	`PF03000.20`	NPH3	218	447	2.9e-55	188.4

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
`Q9LUB9`	Arabidopsis thaliana	BTB/POZ domain-containing protein At5g48130	51.659%	Swiss-Prot	strong database homology
`Q9FNB3`	Arabidopsis thaliana	Putative BTB/POZ domain-containing protein At5g13600	31.884%	Swiss-Prot	moderate database homology
`Q66GP0`	Arabidopsis thaliana	BTB/POZ domain-containing protein SR1IP1	31.377%	Swiss-Prot	moderate database homology
`Q9S9Q9`	Arabidopsis thaliana	BTB/POZ domain-containing protein At1g30440	31.102%	Swiss-Prot	moderate database homology
`Q9FN09`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY3	32.211%	Swiss-Prot	moderate database homology

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