LXL04_012929 | RubberDandelionOmics

Gene overview

LXL04_012929

Reference: OH-1004 Chr: Chr03 Coordinates: 21024107-21028019 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3242 bp · LXL04_012929|LXL04_012929|OH1004|cDNA

ATGGATCAGATAAACTTACTTCACAGTCAAAGGAAAATTCTCCAAGGTCCAGGTGGCAAGTCCTCAACAAGTGGGCCCTCCAAAGATCTATGGCTTGCAGTCCACGGAGGGTCTGTAATCGATGTAGATTCAGCCTTGGTCTCACTGAAGAAAAATGGTGGAAACATCAATTCAAGAAACACATTTGGCCTTACCCCTCTTCATATTGCAACTTGGAGAAATCACATTCCAATCATCAGAAGACTTTTAGCAGCTGGTGC...

CDS

Download CDS FASTA

3219 bp · LXL04_012929|LXL04_012929|OH1004|CDS

ATGGATCAGATAAACTTACTTCACAGTCAAAGGAAAATTCTCCAAGGTCCAGGTGGCAAGTCCTCAACAAGTGGGCCCTCCAAAGATCTATGGCTTGCAGTCCACGGAGGGTCTGTAATCGATGTAGATTCAGCCTTGGTCTCACTGAAGAAAAATGGTGGAAACATCAATTCAAGAAACACATTTGGCCTTACCCCTCTTCATATTGCAACTTGGAGAAATCACATTCCAATCATCAGAAGACTTTTAGCAGCTGGTGC...

Protein

Download Protein FASTA

1072 aa · LXL04_012929|LXL04_012929|OH1004|PROTEIN

MDQINLLHSQRKILQGPGGKSSTSGPSKDLWLAVHGGSVIDVDSALVSLKKNGGNINSRNTFGLTPLHIATWRNHIPIIRRLLAAGADPNARDGESGWSSLHRALHFGHLAVASILLKSEASVAIEDSKSRTPVDLLSGPVLQANGNGDGSVVTELYSWGSGVNYQLGTGNAHIQKLPCKVDSLHGSFIKSISSAKFHSVAVSAHGEVYTWGFGRGGRLGHPDFDIHSGQAAVITPRQVTSGLGARRVKAIAAAKHHTVA...

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_012929`
TK1151 ID	TkA02G529780
OH-1004 ID	LXL04_012929
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
Protein coverage (%)	TK1151 98.339 / OH-1004 99.627 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_012929

Location Chr03:21024107-21028019 (+)

Description Similar to ibtk: Inhibitor of Bruton tyrosine kinase

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_012929 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001933 negative regulation of protein phosphorylation 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:0051209 release of sequestered calcium ion into cytosol Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0016020 membrane Cellular Component

KEGG gene cross-reference

ath:AT5G63860

hsa:25998

xla:431983

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.

Cytoplasm0.527

Rank 1 · LXL04_012929 · OH-1004

Nucleus0.301

Rank 2 · LXL04_012929 · OH-1004

Cell membrane0.191

Rank 3 · LXL04_012929 · OH-1004

Golgi apparatus0.083

Rank 4 · LXL04_012929 · OH-1004

Endoplasmic reticulum0.062

Rank 5 · LXL04_012929 · 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.

PF12796.14Ank_246-126 aa

PF13857.13Ank_552-104 aa

PF00023.37Ank63-93 aa

PF13637.13Ank_474-117 aa

PF25384.2Alsin_RLD152-225 aa

PF25390.2WD40_RLD155-376 aa

PF00415.25RCC1155-202 aa

PF00415.25RCC1206-260 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012929	`PF12796.14`	Ank_2	46	126	9.5e-12	46.0
LXL04_012929	`PF13857.13`	Ank_5	52	104	4.3e-10	40.4
LXL04_012929	`PF00023.37`	Ank	63	93	1.7e-13	50.7
LXL04_012929	`PF13637.13`	Ank_4	74	117	1.7e-12	48.0
LXL04_012929	`PF25384.2`	Alsin_RLD	152	225	6e-16	59.3
LXL04_012929	`PF25390.2`	WD40_RLD	155	376	9.6e-82	275.9
LXL04_012929	`PF00415.25`	RCC1	155	202	1.4e-54	183.1
LXL04_012929	`PF00415.25`	RCC1	206	260	1.4e-54	183.1
LXL04_012929	`PF13540.13`	RCC1_2	248	277	2.2e-26	91.6
LXL04_012929	`PF00415.25`	RCC1	265	312	1.4e-54	183.1
LXL04_012929	`PF25384.2`	Alsin_RLD	267	375	6e-16	59.3
LXL04_012929	`PF25390.2`	WD40_RLD	286	474	9.6e-82	275.9
LXL04_012929	`PF13540.13`	RCC1_2	299	328	2.2e-26	91.6
LXL04_012929	`PF00415.25`	RCC1	315	366	1.4e-54	183.1

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	33.094%	Swiss-Prot	weak database homology
`Q9FJG9`	Arabidopsis thaliana	RCC1 domain-containing protein RUG3, mitochondrial	29.521%	Swiss-Prot	weak database homology

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