LXL04_037898 | RubberDandelionOmics

Gene overview

LXL04_037898

Reference: OH-1004 Chr: Chr09 Coordinates: 24580118-24581669 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1293 bp · LXL04_037898|LXL04_037898|OH1004|cDNA

atgCTTCGCGTTTTGAAGAAATTACCTTTCAATAGCGTCACTCGCCGTCGATGGATGACCACCAGCGCCACCGTGATGAGTTTCGGAGATGGCAGCCATGGTGCTCTAGGCTTACCTACCTCCGTCACCGGAATCGGTTCCGACGCCTACGAACCCACTCCAATCCCATCCCTACCTCCCGACGTCTCCAGCATTGCCGCCGGTCACTACCACTCTCTCGCCGTTACTTCTCAAGGCCACATCTGGTCTTGGGGCCGCAA...

CDS

Download CDS FASTA

1293 bp · LXL04_037898|LXL04_037898|OH1004|CDS

ATGCTTCGCGTTTTGAAGAAATTACCTTTCAATAGCGTCACTCGCCGTCGATGGATGACCACCAGCGCCACCGTGATGAGTTTCGGAGATGGCAGCCATGGTGCTCTAGGCTTACCTACCTCCGTCACCGGAATCGGTTCCGACGCCTACGAACCCACTCCAATCCCATCCCTACCTCCCGACGTCTCCAGCATTGCCGCCGGTCACTACCACTCTCTCGCCGTTACTTCTCAAGGCCACATCTGGTCTTGGGGCCGCAA...

Protein

Download Protein FASTA

430 aa · LXL04_037898|LXL04_037898|OH1004|PROTEIN

MLRVLKKLPFNSVTRRRWMTTSATVMSFGDGSHGALGLPTSVTGIGSDAYEPTPIPSLPPDVSSIAAGHYHSLAVTSQGHIWSWGRNAEGQLGRAIDSPRETWIEPQRIDGLSGVKSAYASGVVSAAIGTDGSVWIWGKSKRGQLGLGIGITDSVTPTRIKALAKEEIVKVSFGWGHALALTKTGKLFGWGYSADGRLGKREITVTSPLDSVTNLSSTLKVEEAEKVVLEAMGKENDMPIIWEPCLINELKDVEVADVSC...

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_037898`
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_037898

Location Chr09:24580118-24581669 (-)

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
`At5g60870`	Regulates DNA damage response (DDR) synergistically with ATM.	The RCC1 family protein RUG3 is required for splicing of nad2 and complex I biogenesis in mitochondria of Arabidopsis thaliana.2011 · DOI: 10.1111/j.1365-313x.2011.04658.x RUG3 and ATM synergistically regulate the alternative splicing of mitochondrial nad2 and the DNA damage response in Arabidopsis thaliana.2017 · DOI: 10.1038/srep43897 RUG3 is a negative regulator of plant responses to ABA in Arabidopsis thaliana.2017 · DOI: 10.1080/15592324.2017.1333217

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_037898 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009411 response to UV Biological Process

GO:0009649 entrainment of circadian clock Biological Process

GO:0010224 response to UV-B Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0003682 chromatin binding Molecular Function

GO:0005085 guanyl-nucleotide exchange factor activity Molecular Function

GO:0009881 photoreceptor activity Molecular Function

GO:0042802 identical protein binding Molecular Function

KEGG gene cross-reference

ath:AT5G63860

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.

Mitochondrion0.753

Rank 1 · LXL04_037898 · OH-1004

Cytoplasm0.125

Rank 2 · LXL04_037898 · OH-1004

Nucleus0.078

Rank 3 · LXL04_037898 · OH-1004

Plastid0.074

Rank 4 · LXL04_037898 · OH-1004

Peroxisome0.032

Rank 5 · LXL04_037898 · 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_RLD25-426 aa

PF00415.25RCC127-75 aa

PF13540.13RCC1_262-91 aa

PF25384.2Alsin_RLD62-110 aa

PF00415.25RCC178-122 aa

PF00415.25RCC1131-181 aa

PF13540.13RCC1_2168-196 aa

PF00415.25RCC1185-268 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037898	`PF25390.2`	WD40_RLD	25	426	4.5e-82	277.0
LXL04_037898	`PF00415.25`	RCC1	27	75	2.1e-71	237.0
LXL04_037898	`PF13540.13`	RCC1_2	62	91	8.3e-43	143.9
LXL04_037898	`PF25384.2`	Alsin_RLD	62	110	6.7e-15	55.8
LXL04_037898	`PF00415.25`	RCC1	78	122	2.1e-71	237.0
LXL04_037898	`PF00415.25`	RCC1	131	181	2.1e-71	237.0
LXL04_037898	`PF13540.13`	RCC1_2	168	196	8.3e-43	143.9
LXL04_037898	`PF00415.25`	RCC1	185	268	2.1e-71	237.0
LXL04_037898	`PF13540.13`	RCC1_2	255	284	8.3e-43	143.9
LXL04_037898	`PF00415.25`	RCC1	271	317	2.1e-71	237.0
LXL04_037898	`PF00415.25`	RCC1	332	376	2.1e-71	237.0
LXL04_037898	`PF13540.13`	RCC1_2	366	391	8.3e-43	143.9
LXL04_037898	`PF00415.25`	RCC1	379	428	2.1e-71	237.0

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	29.620%	Swiss-Prot	weak database homology
`Q9FJG9`	Arabidopsis thaliana	RCC1 domain-containing protein RUG3, mitochondrial	30.227%	Swiss-Prot	moderate database homology

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