LXL04_030647 | RubberDandelionOmics

Gene overview

LXL04_030647

Reference: OH-1004 Chr: Chr06 Coordinates: 120221678-120225722 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2577 bp · LXL04_030647|LXL04_030647|OH1004|cDNA

ATGACTGATCTACAGAAGAATAGCATCGAGGAGCAGAATGTCCAGGAGGCTATTGCTTCTTTGAAAAACTGGTCATATCTACTGAGATATGGACGATTGGGGAAGCCAAGGTTCTTCCCCTTTCGAATCTCTAACGATGAAACAACATTAATCTGGTGTATTTCAAGGAAGGAGAAACATATTCCATTGATTCAAGTCTCTAAGATTATGCGTGGACAACGAACGGCAGTATTCCAACGGTATCCTCAACCTGATAAGGA...

CDS

Download CDS FASTA

2577 bp · LXL04_030647|LXL04_030647|OH1004|CDS

ATGACTGATCTACAGAAGAATAGCATCGAGGAGCAGAATGTCCAGGAGGCTATTGCTTCTTTGAAAAACTGGTCATATCTACTGAGATATGGACGATTGGGGAAGCCAAGGTTCTTCCCCTTTCGAATCTCTAACGATGAAACAACATTAATCTGGTGTATTTCAAGGAAGGAGAAACATATTCCATTGATTCAAGTCTCTAAGATTATGCGTGGACAACGAACGGCAGTATTCCAACGGTATCCTCAACCTGATAAGGA...

Protein

Download Protein FASTA

858 aa · LXL04_030647|LXL04_030647|OH1004|PROTEIN

MTDLQKNSIEEQNVQEAIASLKNWSYLLRYGRLGKPRFFPFRISNDETTLIWCISRKEKHIPLIQVSKIMRGQRTAVFQRYPQPDKEQQSFSVLYGNRSLDVICKDKSEAETWLLALQTLISKNSNSQISKNIDNITSSDGSSSITQRNSTSDILEDSCKYETFTFPISRALSDVLLCTESAKTPPTIIPKSYTSNIHGPRLDDVESLHDVFIWGEGTCDRLLGGGIGTGIGMSNSNSAKIDSLSPKALKRSIAFDARKV...

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_030647`
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_030647

Location Chr06:120221678-120225722 (+)

Description Similar to PRAF1: PH, RCC1 and FYVE domains-containing protein 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g76950`	Binds to phosphatidic acid and to phosphoinositides such as PtdIns3P, PtdIns(3,4)P(2), PtdIns(3,4,5)P(3) and PtdIns(4,5)P(2).	No verified direct reference in this release
`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_030647 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006974 DNA damage response 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:0010374 stomatal complex development Biological Process

GO:0016567 protein ubiquitination Biological Process

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

GO:0045746 negative regulation of Notch signaling pathway Biological Process

GO:0050821 protein stabilization Biological Process

GO:0000785 chromatin Cellular Component

KEGG gene cross-reference

ath:AT1G76950

ath:AT5G63860

mmu:15204

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.

Cytoplasm0.534

Rank 1 · LXL04_030647 · OH-1004

Nucleus0.277

Rank 2 · LXL04_030647 · OH-1004

Cell membrane0.212

Rank 3 · LXL04_030647 · OH-1004

Golgi apparatus0.068

Rank 4 · LXL04_030647 · OH-1004

Lysosome / Vacuole0.064

Rank 5 · LXL04_030647 · 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_RLD210-576 aa

PF13540.13RCC1_2258-283 aa

PF00415.25RCC1273-322 aa

PF13540.13RCC1_2312-332 aa

PF13540.13RCC1_2362-390 aa

PF00415.25RCC1378-427 aa

PF13540.13RCC1_2415-448 aa

PF00415.25RCC1438-484 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030647	`PF25390.2`	WD40_RLD	210	576	7.6e-78	263.1
LXL04_030647	`PF13540.13`	RCC1_2	258	283	4.7e-42	141.5
LXL04_030647	`PF00415.25`	RCC1	273	322	3.2e-71	236.4
LXL04_030647	`PF13540.13`	RCC1_2	312	332	4.7e-42	141.5
LXL04_030647	`PF13540.13`	RCC1_2	362	390	4.7e-42	141.5
LXL04_030647	`PF00415.25`	RCC1	378	427	3.2e-71	236.4
LXL04_030647	`PF13540.13`	RCC1_2	415	448	4.7e-42	141.5
LXL04_030647	`PF00415.25`	RCC1	438	484	3.2e-71	236.4
LXL04_030647	`PF13540.13`	RCC1_2	512	541	4.7e-42	141.5
LXL04_030647	`PF00415.25`	RCC1	530	577	3.2e-71	236.4
LXL04_030647	`PF01363.28`	FYVE	584	647	1.6e-13	51.2

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
`Q947D2`	Arabidopsis thaliana	PH, RCC1 and FYVE domains-containing protein 1	41.911%	Swiss-Prot	moderate database homology
`Q9FN03`	Arabidopsis thaliana	Ultraviolet-B receptor UVR8	36.254%	Swiss-Prot	weak database homology

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