LXL04_012212 | RubberDandelionOmics

Gene overview

LXL04_012212

Reference: OH-1004 Chr: Chr03 Coordinates: 8321566-8326357 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3516 bp · LXL04_012212|LXL04_012212|OH1004|cDNA

ATGGATGTAACTCTACCTCCTCCTCTCATGGTTTCTCAAGGCTTTCTTCCAACTGATTCTCTGTTAGAATCACTCATCCAAATCTCAAATGAAGTAGCATCCATGGAAAAAACCCCAACCACACAATCCAAAAACGTGTCAACAACCATAAGAAGGATCAAGATTCTTTCATCATTGTTCCAAGAGATTCAGGAAACAAACACTCAACTCCCGCCTTCTTCCATTTTGTGTTTGACAGAGCTTTATTCTGTTATTCGGAG...

CDS

Download CDS FASTA

3516 bp · LXL04_012212|LXL04_012212|OH1004|CDS

ATGGATGTAACTCTACCTCCTCCTCTCATGGTTTCTCAAGGCTTTCTTCCAACTGATTCTCTGTTAGAATCACTCATCCAAATCTCAAATGAAGTAGCATCCATGGAAAAAACCCCAACCACACAATCCAAAAACGTGTCAACAACCATAAGAAGGATCAAGATTCTTTCATCATTGTTCCAAGAGATTCAGGAAACAAACACTCAACTCCCGCCTTCTTCCATTTTGTGTTTGACAGAGCTTTATTCTGTTATTCGGAG...

Protein

Download Protein FASTA

1171 aa · LXL04_012212|LXL04_012212|OH1004|PROTEIN

MDVTLPPPLMVSQGFLPTDSLLESLIQISNEVASMEKTPTTQSKNVSTTIRRIKILSSLFQEIQETNTQLPPSSILCLTELYSVIRRVKSLIQECKEGSCLWNLVRAESISNQFYVIVKEMSRALDILPLSLLKIAADTREQVELLHKQVKRVELLLDSKEVQRRDELLQVMMASTKSKSNSKAVIDFEKLKVIMSRIGLKTPFDYEGEISKLEAEAEKEAGTGGLIVVSNINNLISLVSLSKSIVFSREDHKTAEEDKS...

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_012212`
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_012212

Location Chr03:8321566-8326357 (-)

Description Similar to PUB1: U-box domain-containing protein 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g46510`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g29340`	Functions as an E3 ubiquitin ligase.	The E3 ubiquitin ligase activity of arabidopsis PLANT U-BOX17 and its functional tobacco homolog ACRE276 are required for cell death and defense.2006 · DOI: 10.1105/tpc.105.039198
`At3g54850`	Functions as an E3 ubiquitin ligase with specific E2 ubiquitin-conjugating enzymes.	Structure and biochemical function of a prototypical Arabidopsis U-box domain.2004 · DOI: 10.1074/jbc.m405057200

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0102700`	Possesses E3 ubiquitin-protein ligase in vitro.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012212 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002237 response to molecule of bacterial origin Biological Process

GO:0007166 cell surface receptor signaling pathway Biological Process

GO:0009609 response to symbiotic bacterium Biological Process

GO:0009610 response to symbiotic fungus Biological Process

GO:0009877 nodulation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0036377 arbuscular mycorrhizal association Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0050777 negative regulation of immune response Biological Process

GO:0098542 defense response to other organism Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G29340

ath:AT3G46510

ath:AT3G54850

dosa:Os06g0102700

mtr:11430446

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.573

Rank 1 · LXL04_012212 · OH-1004

Nucleus0.366

Rank 2 · LXL04_012212 · OH-1004

Cell membrane0.164

Rank 3 · LXL04_012212 · OH-1004

Endoplasmic reticulum0.056

Rank 4 · LXL04_012212 · OH-1004

Plastid0.036

Rank 5 · LXL04_012212 · 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.

PF19584.4MCAfunc40-162 aa

PF25368.2PUB10_N47-152 aa

PF04564.22U-box276-346 aa

PF25598.2ARM_PUB409-672 aa

PF00514.30Arm423-460 aa

PF24768.2ARM_ARMC5423-612 aa

PF05701.17WEMBL888-1156 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012212	`PF19584.4`	MCAfunc	40	162	1.1e-07	32.4
LXL04_012212	`PF25368.2`	PUB10_N	47	152	5.1e-15	56.9
LXL04_012212	`PF04564.22`	U-box	276	346	3.1e-20	72.8
LXL04_012212	`PF25598.2`	ARM_PUB	409	672	4.9e-24	86.0
LXL04_012212	`PF00514.30`	Arm	423	460	8.1e-25	86.7
LXL04_012212	`PF24768.2`	ARM_ARMC5	423	612	1.1e-10	42.2
LXL04_012212	`PF05701.17`	WEMBL	888	1156	1.6e-11	44.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	39.549%	Swiss-Prot	moderate database homology
`Q9C7R6`	Arabidopsis thaliana	U-box domain-containing protein 17	36.652%	Swiss-Prot	moderate database homology
`Q8VZ40`	Arabidopsis thaliana	U-box domain-containing protein 14	36.818%	Swiss-Prot	moderate database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	36.785%	Swiss-Prot	moderate database homology

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