LXL04_008560 | RubberDandelionOmics

Gene overview

LXL04_008560

Reference: OH-1004 Chr: Chr02 Coordinates: 102779751-102780848 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1098 bp · LXL04_008560|LXL04_008560|OH1004|cDNA

ATGTGGAGTAATCTTCCTTCCGATCTCCTATCCAACATCTTCTCTTACCTTCCACCTCACTCCATCCCCCGCGCCATGGCGGTCTGCCGCCACTGGCGGTCAGCAACCGGCGACACAAAACGGTACCACCGCCACAACCACCACCCGCCATGGTTCATCGCCTTACCCACCCATAGAAACCATTTGTGTTTTATTCATAATCCAATCGAAAACACGTGGCACTCACTCAATCTCAAACATGTTCCTAAATTTATCAGACC...

CDS

Download CDS FASTA

1098 bp · LXL04_008560|LXL04_008560|OH1004|CDS

ATGTGGAGTAATCTTCCTTCCGATCTCCTATCCAACATCTTCTCTTACCTTCCACCTCACTCCATCCCCCGCGCCATGGCGGTCTGCCGCCACTGGCGGTCAGCAACCGGCGACACAAAACGGTACCACCGCCACAACCACCACCCGCCATGGTTCATCGCCTTACCCACCCATAGAAACCATTTGTGTTTTATTCATAATCCAATCGAAAACACGTGGCACTCACTCAATCTCAAACATGTTCCTAAATTTATCAGACC...

Protein

Download Protein FASTA

365 aa · LXL04_008560|LXL04_008560|OH1004|PROTEIN

MWSNLPSDLLSNIFSYLPPHSIPRAMAVCRHWRSATGDTKRYHRHNHHPPWFIALPTHRNHLCFIHNPIENTWHSLNLKHVPKFIRPVSTIGGHGLILFKGATGGVPIQLSVCNPFTGQFGQLPPLQKPRRNPAVGIIEVCPCQFKVYVAGGMSEAATGGGATSYEPTLEMFDSKSEKWTTAGSMPVEFAVRLTVWTPNESVYSNGVLYWMTSARAYSIMGFEISANKWMEFSVPNGYMLEFAALVPRNGKLVVIGGVEG...

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_008560`
TK1151 ID	TkA03G358790
OH-1004 ID	LXL04_008560
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.400
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_008560

Location Chr02:102779751-102780848 (+)

Description Similar to UFO: Protein UNUSUAL FLORAL ORGANS

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g30950`	Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	No verified direct reference in this release
`At5g15710`	F-box/kelch-repeat protein At5g15710.	No verified direct reference in this release
`At1g27340`	F-box only protein 6.	No verified direct reference in this release
`At3g61590`	Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0665400`	Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	ABERRANT PANICLE ORGANIZATION 1 temporally regulates meristem identity in rice.2005 · DOI: 10.1016/j.ydbio.2005.03.016 Rice ABERRANT PANICLE ORGANIZATION 1, encoding an F-box protein, regulates meristem fate.2007 · DOI: 10.1111/j.1365-313x.2007.03200.x Expression level of ABERRANT PANICLE ORGANIZATION1 determines rice inflorescence form through control of cell proliferation in the meristem.2009 · DOI: 10.1104/pp.109.136739 A gene controlling the number of primary rachis branches also controls the vascular bundle formation and hence is responsible to increase the harvest index and grain yield in rice.2010 · DOI: 10.1007/s00122-009-1218-8 New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield.2010 · DOI: 10.1038/ncomms1132 ABERRANT PANICLE ORGANIZATION 2/RFL, the rice ortholog of Arabidopsis LEAFY, suppresses the transition from inflorescence meristem to floral meristem through interaction with APO1.2012 · DOI: 10.1111/j.1365-313x.2011.04781.x Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism.2014 · DOI: 10.1093/mp/ssu131 Ozone-Induced Rice Grain Yield Loss Is Triggered via a Change in Panicle Morphology That Is Controlled by ABERRANT PANICLE ORGANIZATION 1 Gene.2015 · DOI: 10.1371/journal.pone.0123308

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008560 · 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:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009908 flower development Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0009933 meristem structural organization Biological Process

GO:0010074 maintenance of meristem identity Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010193 response to ozone Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0010928 regulation of auxin mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

KEGG gene cross-reference

ath:AT1G27340

ath:AT1G30950

ath:AT3G61590

ath:AT5G15710

osa:107277138

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.

Nucleus0.665

Rank 1 · LXL04_008560 · OH-1004

Cytoplasm0.325

Rank 2 · LXL04_008560 · OH-1004

Cell membrane0.082

Rank 3 · LXL04_008560 · OH-1004

Endoplasmic reticulum0.062

Rank 4 · LXL04_008560 · OH-1004

Plastid0.025

Rank 5 · LXL04_008560 · 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.

PF12937.13F-box-like2-44 aa

PF00646.39F-box2-42 aa

PF13964.13Beta-prop_Calicin65-203 aa

PF08268.18FBA_392-266 aa

PF01344.32Kelch_1146-186 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008560	`PF12937.13`	F-box-like	2	44	1.2e-12	48.1
LXL04_008560	`PF00646.39`	F-box	2	42	4.9e-12	45.9
LXL04_008560	`PF13964.13`	Beta-prop_Calicin	65	203	3e-06	27.2
LXL04_008560	`PF08268.18`	FBA_3	92	266	1.9e-07	31.2
LXL04_008560	`PF01344.32`	Kelch_1	146	186	5.5e-07	29.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q39090`	Arabidopsis thaliana	Protein UNUSUAL FLORAL ORGANS	24.924%	Swiss-Prot	weak database homology
`Q9LFV5`	Arabidopsis thaliana	F-box/kelch-repeat protein At5g15710	24.138%	Swiss-Prot	weak database homology
`Q9FZK1`	Arabidopsis thaliana	F-box only protein 6	25.137%	Swiss-Prot	weak database homology
`Q9M310`	Arabidopsis thaliana	F-box/kelch-repeat protein At3g61590	24.773%	Swiss-Prot	weak database homology
`Q655Y0`	Oryza sativa subsp. japonica	Protein ABERRANT PANICLE ORGANIZATION 1	23.565%	Swiss-Prot	weak database homology

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