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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_024813
Reference: OH-1004 Chr: Chr05 Coordinates: 99443686-99448059 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2868 bp · LXL04_024813|LXL04_024813|OH1004|cDNA

ATGGGTGAAAGATTATTGTCAGTCACTCCCTCTGATAGAGCTCTTGAACAGGCGATCGTGGCTTTAAAGAAAGGGGCATATATATTGAAGTATGGCCGAAGAGGGAAGCCGAAATTATGCCCCTTCAGACTATCAACGGATGAAAGAACTTTAATGTGGTTTTCCGGCAATGAAGAAAAACAACTTCAGCTAAGCTCCGTTAGGAACCTTGTTCGTGGCCATGGGACTAGGAAACTTCAACCAGAAAGAGAATGTCATTC...

CDS

Download CDS FASTA

2868 bp · LXL04_024813|LXL04_024813|OH1004|CDS

ATGGGTGAAAGATTATTGTCAGTCACTCCCTCTGATAGAGCTCTTGAACAGGCGATCGTGGCTTTAAAGAAAGGGGCATATATATTGAAGTATGGCCGAAGAGGGAAGCCGAAATTATGCCCCTTCAGACTATCAACGGATGAAAGAACTTTAATGTGGTTTTCCGGCAATGAAGAAAAACAACTTCAGCTAAGCTCCGTTAGGAACCTTGTTCGTGGCCATGGGACTAGGAAACTTCAACCAGAAAGAGAATGTCATTC...

Protein

Download Protein FASTA

955 aa · LXL04_024813|LXL04_024813|OH1004|PROTEIN

MGERLLSVTPSDRALEQAIVALKKGAYILKYGRRGKPKLCPFRLSTDERTLMWFSGNEEKQLQLSSVRNLVRGHGTRKLQPERECHSFSLIYMNNQAQCSLDLICKDKLQADSWFLGLKALISRCRELGHSENRRGAQSCVNSPSSFLRRKCNMGLSKETTKMSQVRSVCGSPIPESISDRCFSDGLSYSSDSFYSRSSLSSTQNFTENLPPYSPCMKSEEPKKNKNPKSVSRFSTQTTLEVQPNPKRTKLSDVLIWGEG...

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.

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ID Mapping

Input IDLXL04_024813
Source versionOH-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 IDLXL04_024813
LocationChr05:99443686-99448059 (-)
DescriptionSimilar to PRAF1: PH, RCC1 and FYVE domains-containing protein 1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / 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_024813 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0010374 stomatal complex development Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0005737 cytoplasm Cellular Component
GO:0005794 Golgi apparatus Cellular Component
GO:0005829 cytosol Cellular Component
GO:0005886 plasma membrane Cellular Component
GO:0016020 membrane Cellular Component
GO:0005085 guanyl-nucleotide exchange factor activity Molecular Function
GO:0008270 zinc ion binding Molecular Function
GO:0035091 phosphatidylinositol binding Molecular Function
GO:0061630 ubiquitin protein ligase activity Molecular Function
GO:0070300 phosphatidic acid binding Molecular Function
KEGG gene cross-reference
ath:AT1G76950
hsa:8925
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.

Cytoplasm0.517
Rank 1 · LXL04_024813 · OH-1004
Nucleus0.316
Rank 2 · LXL04_024813 · OH-1004
Cell membrane0.237
Rank 3 · LXL04_024813 · OH-1004
Golgi apparatus0.060
Rank 4 · LXL04_024813 · OH-1004
Endoplasmic reticulum0.050
Rank 5 · LXL04_024813 · 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.

PF16457.12PH_1216-122 aa
PF25390.2WD40_RLD253-628 aa
PF00415.25RCC1320-364 aa
PF13540.13RCC1_2351-379 aa
PF00415.25RCC1367-411 aa
PF13540.13RCC1_2398-426 aa
PF00415.25RCC1415-463 aa
PF00415.25RCC1478-525 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_024813PF16457.12PH_12161221.4e-0732.7
LXL04_024813PF25390.2WD40_RLD2536289.9e-74249.5
LXL04_024813PF00415.25RCC13203641.6e-66221.4
LXL04_024813PF13540.13RCC1_23513791.7e-30104.7
LXL04_024813PF00415.25RCC13674111.6e-66221.4
LXL04_024813PF13540.13RCC1_23984261.7e-30104.7
LXL04_024813PF00415.25RCC14154631.6e-66221.4
LXL04_024813PF00415.25RCC14785251.6e-66221.4
LXL04_024813PF25384.2Alsin_RLD5316093.5e-1246.9
LXL04_024813PF13540.13RCC1_25655941.7e-30104.7
LXL04_024813PF00415.25RCC15816301.6e-66221.4
LXL04_024813PF01363.28FYVE6437011.6e-1144.9
LXL04_024813PF08381.17BRX8919468e-2689.9

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.

Download current result

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q947D2Arabidopsis thalianaPH, RCC1 and FYVE domains-containing protein 149.799%Swiss-Protmoderate database homology
Q9FN03Arabidopsis thalianaUltraviolet-B receptor UVR832.796%Swiss-Protweak database homology

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