LXL04_011647 | RubberDandelionOmics

Gene overview

LXL04_011647

Reference: OH-1004 Chr: Chr02 Coordinates: 168825150-168827476 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1626 bp · LXL04_011647|LXL04_011647|OH1004|cDNA

ATGGACGCCACCACGAGTGGAACGCCAACCATTCAATACCACAACATCGCCGACCAACAGATTCCGACCACCGTCGCGGCTTCCACCCCGTCATTTAACCGGCAAACCCGCCATTGTTTTGGCGATGCAACTCCGGGAGAATTCCCATTATCTGCAAACCCCTCAATCGTTCTGCATGTTCTCACTGGTTGTAATCTAGAGCCACAAGATCTCGCAAAACTAGAGGCAAGTTATTCTTTTTTAGCGACATGTTCTTTCTT...

CDS

Download CDS FASTA

1626 bp · LXL04_011647|LXL04_011647|OH1004|CDS

ATGGACGCCACCACGAGTGGAACGCCAACCATTCAATACCACAACATCGCCGACCAACAGATTCCGACCACCGTCGCGGCTTCCACCCCGTCATTTAACCGGCAAACCCGCCATTGTTTTGGCGATGCAACTCCGGGAGAATTCCCATTATCTGCAAACCCCTCAATCGTTCTGCATGTTCTCACTGGTTGTAATCTAGAGCCACAAGATCTCGCAAAACTAGAGGCAAGTTATTCTTTTTTAGCGACATGTTCTTTCTT...

Protein

Download Protein FASTA

541 aa · LXL04_011647|LXL04_011647|OH1004|PROTEIN

MDATTSGTPTIQYHNIADQQIPTTVAASTPSFNRQTRHCFGDATPGEFPLSANPSIVLHVLTGCNLEPQDLAKLEASYSFLATCSFFRQPAHFAPDHELCLSELAALDMCQKRAIFKPMDSEQRHQLKLRCGGSWKLVLRFLLAGETCSRREKSQAIAGPGHSIAVTSKGSVFTFGSNSSGQLGHDTTQEESTPRIIRSLQGIRIIHAAAGAGRTMLISDSGQVYAFGKDSFGEAEYGVQGSKQVNTPKLVESLKDIFVV...

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_011647`
TK1151 ID	TkA03G608590
OH-1004 ID	LXL04_011647
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.900
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011647

Location Chr02:168825150-168827476 (+)

Description Similar to HERC2: E3 ubiquitin-protein ligase HERC2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g63860`	UV-B specific signaling component that acts as a UV-B photoreceptor and plays a key role in establishing UV-protective responses in plants.	A UV-B-specific signaling component orchestrates plant UV protection.2005 · DOI: 10.1073/pnas.0507187102 UV-B promotes rapid nuclear translocation of the Arabidopsis UV-B specific signaling component UVR8 and activates its function in the nucleus.2007 · DOI: 10.1105/tpc.107.053330 UV-B signaling pathways with different fluence-rate response profiles are distinguished in mature Arabidopsis leaf tissue by requirement for UVR8, HY5, and HYH.2008 · DOI: 10.1104/pp.107.108456 Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis.2009 · DOI: 10.1038/emboj.2009.4 UVR8 in Arabidopsis thaliana regulates multiple aspects of cellular differentiation during leaf development in response to ultraviolet B radiation.2009 · DOI: 10.1111/j.1469-8137.2009.02855.x Negative feedback regulation of UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis.2010 · DOI: 10.1073/pnas.0914532107 Functional interaction of the circadian clock and UV RESISTANCE LOCUS 8-controlled UV-B signaling pathways in Arabidopsis thaliana.2011 · DOI: 10.1111/j.1365-313x.2011.04573.x Perception of UV-B by the Arabidopsis UVR8 protein.2011 · DOI: 10.1126/science.1200660 UVR8 mediates UV-B-induced Arabidopsis defense responses against Botrytis cinerea by controlling sinapate accumulation.2012 · DOI: 10.1093/mp/sss025 C-terminal region of the UV-B photoreceptor UVR8 initiates signaling through interaction with the COP1 protein.2012 · DOI: 10.1073/pnas.1210898109 In vivo function of tryptophans in the Arabidopsis UV-B photoreceptor UVR8.2012 · DOI: 10.1105/tpc.112.101451 The UV-B photoreceptor UVR8 promotes photosynthetic efficiency in Arabidopsis thaliana exposed to elevated levels of UV-B.2012 · DOI: 10.1007/s11120-012-9785-y

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011647 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0006974 DNA damage response Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0050821 protein stabilization Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005814 centriole Cellular Component

GO:0005829 cytosol Cellular Component

GO:0016020 membrane Cellular Component

KEGG gene cross-reference

hsa:8924

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.

Cytoplasm0.498

Rank 1 · LXL04_011647 · OH-1004

Nucleus0.332

Rank 2 · LXL04_011647 · OH-1004

Cell membrane0.113

Rank 3 · LXL04_011647 · OH-1004

Mitochondrion0.112

Rank 4 · LXL04_011647 · OH-1004

Endoplasmic reticulum0.062

Rank 5 · LXL04_011647 · 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.

PF25390.2WD40_RLD153-489 aa

PF13540.13RCC1_2158-182 aa

PF00415.25RCC1169-218 aa

PF00415.25RCC1221-272 aa

PF00415.25RCC1275-324 aa

PF00415.25RCC1333-382 aa

PF25384.2Alsin_RLD334-448 aa

PF00415.25RCC1385-434 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011647	`PF25390.2`	WD40_RLD	153	489	4.3e-73	247.4
LXL04_011647	`PF13540.13`	RCC1_2	158	182	4.5e-35	119.3
LXL04_011647	`PF00415.25`	RCC1	169	218	3.8e-68	226.6
LXL04_011647	`PF00415.25`	RCC1	221	272	3.8e-68	226.6
LXL04_011647	`PF00415.25`	RCC1	275	324	3.8e-68	226.6
LXL04_011647	`PF00415.25`	RCC1	333	382	3.8e-68	226.6
LXL04_011647	`PF25384.2`	Alsin_RLD	334	448	8.5e-11	42.3
LXL04_011647	`PF00415.25`	RCC1	385	434	3.8e-68	226.6
LXL04_011647	`PF13540.13`	RCC1_2	422	447	4.5e-35	119.3
LXL04_011647	`PF00415.25`	RCC1	437	488	3.8e-68	226.6
LXL04_011647	`PF25390.2`	WD40_RLD	471	534	4.3e-73	247.4
LXL04_011647	`PF13540.13`	RCC1_2	497	518	4.5e-35	119.3
LXL04_011647	`PF00415.25`	RCC1	506	538	3.8e-68	226.6

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
`Q9FN03`	Arabidopsis thaliana	Ultraviolet-B receptor UVR8	29.581%	Swiss-Prot	weak database homology

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