LXL04_010173 | RubberDandelionOmics

Gene overview

LXL04_010173

Reference: OH-1004 Chr: Chr02 Coordinates: 141437497-141441137 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2292 bp · LXL04_010173|LXL04_010173|OH1004|cDNA

ATGGCCAAACGCGGATATAAGTTGCAGGAATTTGTGGCGCATTCTGCTAATGTGAACTGCATCAAAATCGGAAAGAAATCACGTCGACATTTTATTACAGGAGGCGATGATGAAATTGTTAATATTTGGTCAATTGGTAAAGCCACATCCATAACGAGTTTAATCGGCCACACAAGCCCTATAGAATCTGTAACTTTTGATTCAACTGAAATTTTAGTGGTTGCCGGAGCTTCCTCCGGCGAGATAAAGCTCTGGGACCT...

CDS

Download CDS FASTA

2292 bp · LXL04_010173|LXL04_010173|OH1004|CDS

ATGGCCAAACGCGGATATAAGTTGCAGGAATTTGTGGCGCATTCTGCTAATGTGAACTGCATCAAAATCGGAAAGAAATCACGTCGACATTTTATTACAGGAGGCGATGATGAAATTGTTAATATTTGGTCAATTGGTAAAGCCACATCCATAACGAGTTTAATCGGCCACACAAGCCCTATAGAATCTGTAACTTTTGATTCAACTGAAATTTTAGTGGTTGCCGGAGCTTCCTCCGGCGAGATAAAGCTCTGGGACCT...

Protein

Download Protein FASTA

763 aa · LXL04_010173|LXL04_010173|OH1004|PROTEIN

MAKRGYKLQEFVAHSANVNCIKIGKKSRRHFITGGDDEIVNIWSIGKATSITSLIGHTSPIESVTFDSTEILVVAGASSGEIKLWDLEETKVVRTLDGHRSYCTALEFHPFGEFLASGSMDTNLKIWDIRKKGCIHTYKGHKRAISTIRFTPDGRWVVSGGLDNVVKIWDLTAGKLLHEFKLHEGHIKSMDFHPLEFLLATGSSDRTVKFWDLETFELIGTTRPEGTGVRSITFHPDGRTLFCGLDNSLKVYSWEPMICH...

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_010173`
TK1151 ID	TkA03G508660
OH-1004 ID	LXL04_010173
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	97.900
Protein coverage (%)	TK1151 81.832 / OH-1004 69.069 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_010173

Location Chr02:141437497-141441137 (-)

Description Similar to At5g23430: Katanin p80 WD40 repeat-containing subunit B1 homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g61210`	May participate in a complex which severs microtubules in an ATP-dependent manner (By similarity).	DWA3, an Arabidopsis DWD protein, acts as a negative regulator in ABA signal transduction.2011 · DOI: 10.1016/j.plantsci.2010.10.008
`At1g11160`	May participate in a complex which severs microtubules in an ATP-dependent manner (By similarity).	No verified direct reference in this release
`At5g23430`	May participate in a complex which severs microtubules in an ATP-dependent manner (By similarity).	No verified direct reference in this release
`At5g08390`	May participate in a complex which severs microtubules in an ATP-dependent manner (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010173 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007019 microtubule depolymerization Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0051013 microtubule severing Biological Process

GO:0051510 regulation of unidimensional cell growth Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005874 microtubule Cellular Component

GO:0008352 katanin complex Cellular Component

GO:0015630 microtubule cytoskeleton Cellular Component

GO:0080008 Cul4-RING E3 ubiquitin ligase complex Cellular Component

GO:0008017 microtubule binding Molecular Function

KEGG gene cross-reference

ath:AT1G11160

ath:AT1G61210

ath:AT5G23430

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.

Cytoplasm0.670

Rank 1 · LXL04_010173 · OH-1004

Nucleus0.192

Rank 2 · LXL04_010173 · OH-1004

Cell membrane0.132

Rank 3 · LXL04_010173 · OH-1004

Golgi apparatus0.113

Rank 4 · LXL04_010173 · OH-1004

Lysosome / Vacuole0.086

Rank 5 · LXL04_010173 · 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.

PF23381.2Beta-prop_IFT122_1st3-121 aa

PF25173.2Beta-prop_WDR3_1st3-142 aa

PF23409.2Beta-prop_EML4-129 aa

PF25175.2Beta-prop_WDR55-137 aa

PF24782.3WD40_MABP1-WDR62_2nd6-171 aa

PF25174.2Beta-prop_THOC37-67 aa

PF25391.2WD40_Gbeta9-133 aa

PF25047.1Beta-prop_TEP1_2nd9-128 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010173	`PF23381.2`	Beta-prop_IFT122_1st	3	121	5.2e-57	194.0
LXL04_010173	`PF25173.2`	Beta-prop_WDR3_1st	3	142	1.3e-52	178.9
LXL04_010173	`PF23409.2`	Beta-prop_EML	4	129	4e-16	60.0
LXL04_010173	`PF25175.2`	Beta-prop_WDR5	5	137	5.1e-61	207.2
LXL04_010173	`PF24782.3`	WD40_MABP1-WDR62_2nd	6	171	9.4e-17	61.7
LXL04_010173	`PF25174.2`	Beta-prop_THOC3	7	67	1e-59	202.5
LXL04_010173	`PF25391.2`	WD40_Gbeta	9	133	4.2e-29	102.3
LXL04_010173	`PF25047.1`	Beta-prop_TEP1_2nd	9	128	6.3e-20	72.1
LXL04_010173	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	12	132	1.4e-31	110.7
LXL04_010173	`PF24796.2`	WDR55	13	93	1.1e-24	87.7
LXL04_010173	`PF24814.2`	WD40_Prp19	14	253	6.2e-48	164.0
LXL04_010173	`PF24817.2`	WD40_WDHD1_1st	15	101	2.7e-46	158.8
LXL04_010173	`PF29037.1`	DSE1_N	15	89	3.5e-19	69.9
LXL04_010173	`PF24017.3`	Beta-prop_SCAP	25	106	2.1e-14	54.0
LXL04_010173	`PF23393.3`	Beta-prop_WDR90_POC16_2nd	26	132	2.2e-25	90.2
LXL04_010173	`PF23414.2`	Beta-prop_EML_2	27	157	5.9e-30	105.3

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
`F4HTH8`	Arabidopsis thaliana	Katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.2	72.480%	Swiss-Prot	weak database homology
`A0A1P8AW69`	Arabidopsis thaliana	Katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.1	70.370%	Swiss-Prot	weak database homology
`Q8H0T9`	Arabidopsis thaliana	Katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.4	70.333%	Swiss-Prot	weak database homology
`F4KB17`	Arabidopsis thaliana	Katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.3	70.530%	Swiss-Prot	weak database homology

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