LXL04_005251 | RubberDandelionOmics

Gene overview

LXL04_005251

Reference: OH-1004 Chr: Chr01 Coordinates: 158904924-158907028 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1692 bp · LXL04_005251|LXL04_005251|OH1004|cDNA

ATGGCGGAGGCTGAAATATATGCTGATTCAGGTAGTCTCTCTCGGAAAGTAGTGACTGTTTCTGCCGGAGAAGCACATACTCTCGCTCTCACAGCTTTTGGTGTgatgtttgattttgattttatGCGAGAAGGCGATGGGAGTGTTTATTCATGGGGAAGAGGAACTTTCGGCCGCCTTGGTGCCGGTTCGGAAGTCGATCGGCTTTTTCCGGCAAAAGTTGAATTCAATTCCGCAGATACGAGAGGAAATGTCAAAAT...

CDS

Download CDS FASTA

1692 bp · LXL04_005251|LXL04_005251|OH1004|CDS

ATGGCGGAGGCTGAAATATATGCTGATTCAGGTAGTCTCTCTCGGAAAGTAGTGACTGTTTCTGCCGGAGAAGCACATACTCTCGCTCTCACAGCTTTTGGTGTGATGTTTGATTTTGATTTTATGCGAGAAGGCGATGGGAGTGTTTATTCATGGGGAAGAGGAACTTTCGGCCGCCTTGGTGCCGGTTCGGAAGTCGATCGGCTTTTTCCGGCAAAAGTTGAATTCAATTCCGCAGATACGAGAGGAAATGTCAAAAT...

Protein

Download Protein FASTA

563 aa · LXL04_005251|LXL04_005251|OH1004|PROTEIN

MAEAEIYADSGSLSRKVVTVSAGEAHTLALTAFGVMFDFDFMREGDGSVYSWGRGTFGRLGAGSEVDRLFPAKVEFNSADTRGNVKIVQVSAGAYHSLALSDDGSIWSWGHNTYGQLGVNGENSLVPSLVQMFHELHPPTSITDHESITETETRLQISSIKAGGMMSLAIDNLGSLWTWGNCPSQDTLTENEFSLISTYTPIPIWNFHGQTVVKVSCGNEHIVALVTTGETHNGDNLLCYSWGNNNHGQLGLGDTEFRTT...

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_005251`
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_005251

Location Chr01:158904924-158907028 (-)

Description Similar to UVR8: Ultraviolet-B receptor UVR8

Arabidopsis / Rice Reference Genes and Papers

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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_005251 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0009411 response to UV Biological Process

GO:0009649 entrainment of circadian clock Biological Process

GO:0010224 response to UV-B Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0030154 cell differentiation Biological Process

GO:0045879 negative regulation of smoothened signaling pathway Biological Process

GO:0000785 chromatin Cellular Component

GO:0001650 fibrillar center Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT5G63860

mmu:67345

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.

Cytoplasm0.447

Rank 1 · LXL04_005251 · OH-1004

Nucleus0.417

Rank 2 · LXL04_005251 · OH-1004

Mitochondrion0.088

Rank 3 · LXL04_005251 · OH-1004

Peroxisome0.062

Rank 4 · LXL04_005251 · OH-1004

Cell membrane0.061

Rank 5 · LXL04_005251 · 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.

PF00415.25RCC146-100 aa

PF25390.2WD40_RLD49-437 aa

PF13540.13RCC1_287-116 aa

PF00415.25RCC1103-135 aa

PF13540.13RCC1_2212-249 aa

PF00415.25RCC1239-287 aa

PF00415.25RCC1300-346 aa

PF00415.25RCC1350-404 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005251	`PF00415.25`	RCC1	46	100	2.2e-65	217.7
LXL04_005251	`PF25390.2`	WD40_RLD	49	437	3.8e-69	234.5
LXL04_005251	`PF13540.13`	RCC1_2	87	116	1.2e-36	124.3
LXL04_005251	`PF00415.25`	RCC1	103	135	2.2e-65	217.7
LXL04_005251	`PF13540.13`	RCC1_2	212	249	1.2e-36	124.3
LXL04_005251	`PF00415.25`	RCC1	239	287	2.2e-65	217.7
LXL04_005251	`PF00415.25`	RCC1	300	346	2.2e-65	217.7
LXL04_005251	`PF00415.25`	RCC1	350	404	2.2e-65	217.7
LXL04_005251	`PF13540.13`	RCC1_2	392	420	1.2e-36	124.3

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	28.798%	Swiss-Prot	weak database homology

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