LXL04_027841 | RubberDandelionOmics

Gene overview

LXL04_027841

Reference: OH-1004 Chr: Chr06 Coordinates: 24608189-24609317 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

963 bp · LXL04_027841|LXL04_027841|OH1004|cDNA

ATGAAGCTCGCATGGCTAAGGTCTCTAGAAACTTCTCACCAAGATTGCGTCTGGGCTTGTACATGGGTCCCTGCCACGGATAAAAGCCCCGGCCTCCTCCTCACCGGATCCCTCGACGAGACGGTGAAGCTATGGAATCCGGAGGACCTCTCCCTTGTCCGTACCAACACCGGACACTGCCTCGGCGTCGTCTCCGTAGCTGCTCATCCTTCCGGTAAAATCGCCGCCTCCGCTTCCATGGACAGCTTCATCCGTGTATT...

CDS

Download CDS FASTA

963 bp · LXL04_027841|LXL04_027841|OH1004|CDS

ATGAAGCTCGCATGGCTAAGGTCTCTAGAAACTTCTCACCAAGATTGCGTCTGGGCTTGTACATGGGTCCCTGCCACGGATAAAAGCCCCGGCCTCCTCCTCACCGGATCCCTCGACGAGACGGTGAAGCTATGGAATCCGGAGGACCTCTCCCTTGTCCGTACCAACACCGGACACTGCCTCGGCGTCGTCTCCGTAGCTGCTCATCCTTCCGGTAAAATCGCCGCCTCCGCTTCCATGGACAGCTTCATCCGTGTATT...

Protein

Download Protein FASTA

320 aa · LXL04_027841|LXL04_027841|OH1004|PROTEIN

MKLAWLRSLETSHQDCVWACTWVPATDKSPGLLLTGSLDETVKLWNPEDLSLVRTNTGHCLGVVSVAAHPSGKIAASASMDSFIRVFDVESNNTIATLEAPPSEVWQMQFDPRGTTLAVAGGSSASVKLWDTAEWKLISTLSIPRPEASKPSDKGNNKKFVLSVAWSSNGRQLACGSMDGSISVFDVQRSKFLHHLDGHTMPVRSLAYSPLDPRVLVSGSDDERIHMYDAEGKTLFSSMSGHSGWVLSVDVSPDGAAIAS...

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_027841`
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_027841

Location Chr06:24608189-24609317 (-)

Description Similar to VIP3: WD repeat-containing protein VIP3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g29830`	Component of the PAF1 complex (PAF1C) which is involved in histone modifications such as methylation on histone H3 'Lys-4' (H3K4me3).	Genetic analysis of early flowering mutants in Arabidopsis defines a class of pleiotropic developmental regulator required for expression of the flowering-time switch flowering locus C.2003 · DOI: 10.1093/genetics/164.1.347 Non conservation of the meiotic function of the Ski8/Rec103 homolog in Arabidopsis.2006 · DOI: 10.1111/j.1365-2443.2006.00972.x Context-dependent dual role of SKI8 homologs in mRNA synthesis and turnover.2012 · DOI: 10.1371/journal.pgen.1002652 Enhancement of meristem formation by bouquet-1, a mis-sense allele of the vernalization independence 3 gene encoding a WD40 repeat protein in Arabidopsis thaliana.2012 · DOI: 10.1111/gtc.12014

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027841 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0009908 flower development Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0016441 post-transcriptional gene silencing Biological Process

GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Biological Process

GO:0072344 rescue of stalled cytosolic ribosome Biological Process

GO:1904278 positive regulation of wax biosynthetic process Biological Process

GO:0000791 euchromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT4G29830

dre:393827

gga:415359

xla:444484

xtr:394466

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.

Nucleus0.695

Rank 1 · LXL04_027841 · OH-1004

Cytoplasm0.420

Rank 2 · LXL04_027841 · OH-1004

Mitochondrion0.038

Rank 3 · LXL04_027841 · OH-1004

Cell membrane0.038

Rank 4 · LXL04_027841 · OH-1004

Lysosome / Vacuole0.027

Rank 5 · LXL04_027841 · 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.

PF25047.1Beta-prop_TEP1_2nd6-130 aa

PF25172.2Beta-prop_WDR3_2nd8-88 aa

PF25460.2Beta-prop_Aladin8-136 aa

PF24814.2WD40_Prp1912-198 aa

PF25173.2Beta-prop_WDR3_1st13-131 aa

PF24105.2Beta-prop_CAF1B_HIR113-97 aa

PF24807.2WD40_CDC20-Fz14-136 aa

PF23381.2Beta-prop_IFT122_1st16-318 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027841	`PF25047.1`	Beta-prop_TEP1_2nd	6	130	1.7e-20	74.0
LXL04_027841	`PF25172.2`	Beta-prop_WDR3_2nd	8	88	1.6e-34	120.2
LXL04_027841	`PF25460.2`	Beta-prop_Aladin	8	136	2.9e-12	47.1
LXL04_027841	`PF24814.2`	WD40_Prp19	12	198	4.5e-44	151.3
LXL04_027841	`PF25173.2`	Beta-prop_WDR3_1st	13	131	3.3e-51	174.3
LXL04_027841	`PF24105.2`	Beta-prop_CAF1B_HIR1	13	97	8.8e-22	78.3
LXL04_027841	`PF24807.2`	WD40_CDC20-Fz	14	136	9.9e-40	137.4
LXL04_027841	`PF23381.2`	Beta-prop_IFT122_1st	16	318	7e-49	167.3
LXL04_027841	`PF23414.2`	Beta-prop_EML_2	25	137	3.8e-28	99.3
LXL04_027841	`PF25174.2`	Beta-prop_THOC3	26	99	6.4e-56	190.1
LXL04_027841	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	26	147	2.4e-21	77.1
LXL04_027841	`PF23393.3`	Beta-prop_WDR90_POC16_2nd	27	134	3.3e-18	66.7
LXL04_027841	`PF24817.2`	WD40_WDHD1_1st	28	210	4.2e-35	122.1
LXL04_027841	`PF25175.2`	Beta-prop_WDR5	31	142	2.2e-56	192.0
LXL04_027841	`PF24805.2`	EIF3I	32	231	1.5e-22	80.9
LXL04_027841	`PF25391.2`	WD40_Gbeta	33	132	1.7e-23	83.9

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
`Q9SZQ5`	Arabidopsis thaliana	WD repeat-containing protein VIP3	74.766%	Swiss-Prot	strong database homology

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