LXL04_026958 | RubberDandelionOmics

Gene overview

LXL04_026958

Reference: OH-1004 Chr: Chr06 Coordinates: 5882086-5885596 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1780 bp · LXL04_026958|LXL04_026958|OH1004|cDNA

ATGACTACATGTTTACGTAtatatattgatatatatatcTCATGTATCTATGATATATAATGCAGATTTATCAAGATCAAAGATGAAGTTTATGCGACTTGGTACAAGGCCAGACAACTTTTATACGGAAGAAGCCATTAGGacaatatattcagactcacCAAGTGATCTAACCATACATGTCAACAACATCACCTATCTTCTCCATAAGTTTCCACTTGTTCCAAAGTGCGGCCTCTTACAGAGACTTTGCTCTGATA...

CDS

Download CDS FASTA

1755 bp · LXL04_026958|LXL04_026958|OH1004|CDS

TTGATATATATATCTCATGTATCTATGATATATAATGCAGATTTATCAAGATCAAAGATGAAGTTTATGCGACTTGGTACAAGGCCAGACAACTTTTATACGGAAGAAGCCATTAGGACAATATATTCAGACTCACCAAGTGATCTAACCATACATGTCAACAACATCACCTATCTTCTCCATAAGTTTCCACTTGTTCCAAAGTGCGGCCTCTTACAGAGACTTTGCTCTGATAGGAGTGATTGTAGCAGATTAGTTCT...

Protein

Download Protein FASTA

584 aa · LXL04_026958|LXL04_026958|OH1004|PROTEIN

MIYISHVSMIYNADLSRSKMKFMRLGTRPDNFYTEEAIRTIYSDSPSDLTIHVNNITYLLHKFPLVPKCGLLQRLCSDRSDCSRLVLELHDIPGGEDAFELCAKFCYGIAIDLSAHNFVRAICAAKFLQMTESIEKGNFASKLEAFFNSCILEGWKDSVVTLQTTRTLPEWSENLGIIRKCIDSVVEKILTPPTKVKWSYTYTREGYSKKKHHHSAPKDWWTEDIANLDIDLFRCVLNTVKLTNTLPPQLIGESLHVYSS...

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_026958`
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_026958

Location Chr06:5882086-5885596 (+)

Description Similar to At5g47800: BTB/POZ domain-containing protein At5g47800

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g47800`	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
`At1g67900`	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
`At4g31820`	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).	NPY1, a BTB-NPH3-like protein, plays a critical role in auxin-regulated organogenesis in Arabidopsis.2007 · DOI: 10.1073/pnas.0708506104 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 Polar-localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers.2011 · DOI: 10.1242/dev.057745 MAB4-induced auxin sink generates local auxin gradients in Arabidopsis organ formation.2014 · DOI: 10.1073/pnas.1316109111 AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells.2021 · DOI: 10.1016/j.cub.2021.02.028
`At3g26490`	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_026958 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009908 flower development Biological Process

GO:0009911 positive regulation of flower development Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0010229 inflorescence development Biological Process

GO:0010540 basipetal auxin transport Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0045176 apical protein localization Biological Process

GO:0048825 cotyledon development 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

KEGG gene cross-reference

ath:AT1G67900

ath:AT3G26490

ath:AT4G31820

ath:AT5G47800

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.

Nucleus0.526

Rank 1 · LXL04_026958 · OH-1004

Cytoplasm0.347

Rank 2 · LXL04_026958 · OH-1004

Cell membrane0.149

Rank 3 · LXL04_026958 · OH-1004

Endoplasmic reticulum0.054

Rank 4 · LXL04_026958 · OH-1004

Lysosome / Vacuole0.034

Rank 5 · LXL04_026958 · 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.

PF03000.20NPH3219-461 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026958	`PF03000.20`	NPH3	219	461	2.5e-74	250.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FIK1`	Arabidopsis thaliana	BTB/POZ domain-containing protein At5g47800	53.430%	Swiss-Prot	strong database homology
`Q9C9V6`	Arabidopsis thaliana	BTB/POZ domain-containing protein At1g67900	43.833%	Swiss-Prot	moderate database homology
`Q8H1D3`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY1	37.409%	Swiss-Prot	moderate database homology
`Q9LIM6`	Arabidopsis thaliana	BTB/POZ domain-containing protein At3g26490	38.899%	Swiss-Prot	moderate database homology
`Q9FN09`	Arabidopsis thaliana	Phototropic-responsive NPH3 family protein NPY3	38.039%	Swiss-Prot	moderate database homology

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