LXL04_022015 | RubberDandelionOmics

Gene overview

LXL04_022015

Reference: OH-1004 Chr: Chr04 Coordinates: 142454821-142458782 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1884 bp · LXL04_022015|LXL04_022015|OH1004|cDNA

ATGGACGATATCGTGCCGGAATACAAGAAAAGAATGGCACGTTTTAGAATACAAGAACTCAAGGATGTTCTTGCCCAACTTGGTCTTCCAAGAACCGGGAGGAAGCAGAAGGTAGTAAATTGTTATATAACCTTCTTTTTTTCAAGatttcttcttttttttctCCTCATTTTGTTTCTGTTACCAGATACTAATTGTCCACAAAAGAACAAACCTATCCAAAAGGAAGATGTAACAAAGATAATCGATGAAACTTATAg...

CDS

Download CDS FASTA

1884 bp · LXL04_022015|LXL04_022015|OH1004|CDS

ATGGACGATATCGTGCCGGAATACAAGAAAAGAATGGCACGTTTTAGAATACAAGAACTCAAGGATGTTCTTGCCCAACTTGGTCTTCCAAGAACCGGGAGGAAGCAGAAGGTAGTAAATTGTTATATAACCTTCTTTTTTTCAAGATTTCTTCTTTTTTTTCTCCTCATTTTGTTTCTGTTACCAGATACTAATTGTCCACAAAAGAACAAACCTATCCAAAAGGAAGATGTAACAAAGATAATCGATGAAACTTATAG...

Protein

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627 aa · LXL04_022015|LXL04_022015|OH1004|PROTEIN

MDDIVPEYKKRMARFRIQELKDVLAQLGLPRTGRKQKVVNCYITFFFSRFLLFFLLILFLLPDTNCPQKNKPIQKEDVTKIIDETYRNMPHSGPIEPITGGNSNCVSDTSSIKPKKEIMDQKIRCPCGSRLKTEFMIQCSDPQCHVLQHIPCVIIPLESTEEVPFLSSQHYCEICRIDRCDPFWKSLAHPLYPVKLCVSNAMDDDSQLVQNVETIFKITRENVHILEKSGYDVQAWCMLLNDSVPFRMQWPQYPDLKVNG...

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_022015`
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_022015

Location Chr04:142454821-142458782 (+)

Description Similar to SIZ1: E3 SUMO-protein ligase SIZ1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g60410`	E3 SUMO protein ligase involved in regulation processes.	The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses.2005 · DOI: 10.1073/pnas.0500778102 SIZ1 small ubiquitin-like modifier E3 ligase facilitates basal thermotolerance in Arabidopsis independent of salicylic acid.2006 · DOI: 10.1104/pp.106.088831 Salicylic acid-mediated innate immunity in Arabidopsis is regulated by SIZ1 SUMO E3 ligase.2007 · DOI: 10.1111/j.1365-313x.2006.02947.x SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis.2007 · DOI: 10.1105/tpc.106.048397 Genetic analysis of SUMOylation in Arabidopsis: conjugation of SUMO1 and SUMO2 to nuclear proteins is essential.2007 · DOI: 10.1104/pp.107.102285 The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses.2007 · DOI: 10.1105/tpc.106.049981 The PHD domain of plant PIAS proteins mediates sumoylation of bromodomain GTE proteins.2008 · DOI: 10.1074/jbc.m708176200 Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates abscisic acid signaling.2009 · DOI: 10.1073/pnas.0811088106 SUMOylation represses SnRK1 signaling in Arabidopsis.2016 · DOI: 10.1111/tpj.13096

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0719100`	Probable SUMO E3 ligase that may regulate Pi starvation responses.	No verified direct reference in this release
`Os05g0125000`	Probable SUMO E3 ligase that may regulate Pi starvation responses.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_022015 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002758 innate immune response-activating signaling pathway Biological Process

GO:0006281 DNA repair Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006952 defense response Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009553 embryo sac development Biological Process

GO:0009787 regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0010113 negative regulation of systemic acquired resistance Biological Process

KEGG gene cross-reference

ath:AT5G60410

cel:CELE_W10D5.3

dosa:Os03g0719100

dosa:Os05g0125000

spo:2541580

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.

Nucleus0.814

Rank 1 · LXL04_022015 · OH-1004

Cytoplasm0.300

Rank 2 · LXL04_022015 · OH-1004

Mitochondrion0.037

Rank 3 · LXL04_022015 · OH-1004

Cell membrane0.030

Rank 4 · LXL04_022015 · OH-1004

Endoplasmic reticulum0.018

Rank 5 · LXL04_022015 · 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.

PF02891.27zf-MIZ371-419 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022015	`PF02891.27`	zf-MIZ	371	419	6.9e-16	58.5

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
`Q680Q4`	Arabidopsis thaliana	E3 SUMO-protein ligase SIZ1	45.860%	Swiss-Prot	moderate database homology
`Q6ASW7`	Oryza sativa subsp. japonica	E3 SUMO-protein ligase SIZ2	43.907%	Swiss-Prot	moderate database homology
`Q6L4L4`	Oryza sativa subsp. japonica	E3 SUMO-protein ligase SIZ1	42.226%	Swiss-Prot	moderate database homology

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