LXL04_038463 | RubberDandelionOmics

Gene overview

LXL04_038463

Reference: OH-1004 Chr: Chr09 Coordinates: 41785441-41790107 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2448 bp · LXL04_038463|LXL04_038463|OH1004|cDNA

ATGGCAATCGATATCAAAACCCTAAAGGATAGGTATATTGATTCTTGCAAAGCTTGTGAAACCATTCCTAATAAAGCTGTTCTGTCAGCTCTCTTTAAGGCTGAAGTTAAGAAATCTAATAATGAAGAGTCCATTTTTTTAATCTACTTAGATGACTTCAAATCCATCGACTTTCATCCACTTTACAATCTATTTCTCCAAATTGATCTATCAGAAATAGACTCAGTTGACATACTCCAAAAATCATCATGTTCATTAGA...

CDS

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2448 bp · LXL04_038463|LXL04_038463|OH1004|CDS

ATGGCAATCGATATCAAAACCCTAAAGGATAGGTATATTGATTCTTGCAAAGCTTGTGAAACCATTCCTAATAAAGCTGTTCTGTCAGCTCTCTTTAAGGCTGAAGTTAAGAAATCTAATAATGAAGAGTCCATTTTTTTAATCTACTTAGATGACTTCAAATCCATCGACTTTCATCCACTTTACAATCTATTTCTCCAAATTGATCTATCAGAAATAGACTCAGTTGACATACTCCAAAAATCATCATGTTCATTAGA...

Protein

Download Protein FASTA

815 aa · LXL04_038463|LXL04_038463|OH1004|PROTEIN

MAIDIKTLKDRYIDSCKACETIPNKAVLSALFKAEVKKSNNEESIFLIYLDDFKSIDFHPLYNLFLQIDLSEIDSVDILQKSSCSLDGDSVLLLLHAINQKLRVVDLQDRTFGKDFLMGLSLGGMSCQILNLKFSHFRKINMIGKFIQIRTLNLDFSASLTNFGKDCFSCMPNLKSLSLCETKVSNLWTTSASLAKLPSLIELRFQSCLCCDDTRVCPRSFGVKADENTSPSSSSSSSILDRGFEKITPFLTTEENTSLF...

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_038463`
TK1151 ID	TkA04G432540
OH-1004 ID	LXL04_038463
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

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Basic Information and Functional Annotation

Gene ID LXL04_038463

Location Chr09:41785441-41790107 (-)

Description Similar to KATNB1: Katanin p80 WD40 repeat-containing subunit B1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34280`	May act as a substrate receptor of a CUL4-RING E3 ubiquitin- protein ligase (CRL4) complex involved in the negative regulation of cellular responses to ultraviolet-B (UV-B) illumination, likely in coordination with RUP1.	DWD HYPERSENSITIVE TO UV-B 1 is negatively involved in UV-B mediated cellular responses in Arabidopsis.2014 · DOI: 10.1007/s11103-014-0247-0 DHU1 negatively regulates UV-B signaling via its direct interaction with COP1 and RUP1.2017 · DOI: 10.1016/j.bbrc.2017.07.110

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_038463 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007019 microtubule depolymerization Biological Process

GO:0010224 response to UV-B Biological Process

GO:0051013 microtubule severing Biological Process

GO:0051301 cell division Biological Process

GO:0071493 cellular response to UV-B Biological Process

GO:0000922 spindle pole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005813 centrosome Cellular Component

GO:0005819 spindle Cellular Component

KEGG gene cross-reference

ath:AT4G34280

gga:415631

mmu:69544

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.

Nucleus0.509

Rank 1 · LXL04_038463 · OH-1004

Cytoplasm0.402

Rank 2 · LXL04_038463 · OH-1004

Cell membrane0.074

Rank 3 · LXL04_038463 · OH-1004

Mitochondrion0.066

Rank 4 · LXL04_038463 · OH-1004

Lysosome / Vacuole0.045

Rank 5 · LXL04_038463 · 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.

PF20919.3DHU1_N4-405 aa

PF23098.2Beta-prop_NOL10_N478-648 aa

PF24814.2WD40_Prp19481-684 aa

PF24817.2WD40_WDHD1_1st489-651 aa

PF25172.2Beta-prop_WDR3_2nd489-685 aa

PF25171.2Beta-prop_WDR36-Utp21_1st493-686 aa

PF23775.2Beta-prop_RIG_2nd526-657 aa

PF25175.2Beta-prop_WDR5536-730 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038463	`PF20919.3`	DHU1_N	4	405	7.1e-74	250.0
LXL04_038463	`PF23098.2`	Beta-prop_NOL10_N	478	648	5e-10	39.8
LXL04_038463	`PF24814.2`	WD40_Prp19	481	684	1.5e-15	57.7
LXL04_038463	`PF24817.2`	WD40_WDHD1_1st	489	651	5.3e-11	43.0
LXL04_038463	`PF25172.2`	Beta-prop_WDR3_2nd	489	685	1e-08	35.5
LXL04_038463	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	493	686	5.7e-14	52.9
LXL04_038463	`PF23775.2`	Beta-prop_RIG_2nd	526	657	9e-09	35.9
LXL04_038463	`PF25175.2`	Beta-prop_WDR5	536	730	1.2e-18	68.2
LXL04_038463	`PF23414.2`	Beta-prop_EML_2	537	683	9.4e-08	32.5
LXL04_038463	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	538	685	1.4e-06	28.5
LXL04_038463	`PF24807.2`	WD40_CDC20-Fz	571	683	7.8e-13	49.1
LXL04_038463	`PF25174.2`	Beta-prop_THOC3	575	684	7.8e-17	61.9
LXL04_038463	`PF25173.2`	Beta-prop_WDR3_1st	576	684	7.9e-14	52.5
LXL04_038463	`PF23381.2`	Beta-prop_IFT122_1st	583	682	3.1e-13	50.4
LXL04_038463	`PF24796.2`	WDR55	585	683	6.9e-09	35.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8GYY7`	Arabidopsis thaliana	Protein DWD HYPERSENSITIVE TO UV-B 1	51.351%	Swiss-Prot	strong database homology

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