LXL04_016122 | RubberDandelionOmics

Gene overview

LXL04_016122

Reference: OH-1004 Chr: Chr03 Coordinates: 111296753-111301351 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3813 bp · LXL04_016122|LXL04_016122|OH1004|cDNA

ATGGCTTCCCCTGGAAACCAGAACCAACAACTAGGTGGAGGACCATTCGATGTTCAAAGATTATTCAATCCTTCTTCTTCCCCACCACCAATCACAACAAACCCTAATACCACCTTCCAAAACCCTAACATCCCTTATCCTCCACCATCATCTGCCGCCTCGTATCCTCCACCCACCGTCACCGGTGCGCTTTACTCATACTCTCCTCAAACTAACCCTATTTACCACCCTCAATTTCATATCCCGTCACCCCCTTTTCA...

CDS

Download CDS FASTA

3813 bp · LXL04_016122|LXL04_016122|OH1004|CDS

ATGGCTTCCCCTGGAAACCAGAACCAACAACTAGGTGGAGGACCATTCGATGTTCAAAGATTATTCAATCCTTCTTCTTCCCCACCACCAATCACAACAAACCCTAATACCACCTTCCAAAACCCTAACATCCCTTATCCTCCACCATCATCTGCCGCCTCGTATCCTCCACCCACCGTCACCGGTGCGCTTTACTCATACTCTCCTCAAACTAACCCTATTTACCACCCTCAATTTCATATCCCGTCACCCCCTTTTCA...

Protein

Download Protein FASTA

1270 aa · LXL04_016122|LXL04_016122|OH1004|PROTEIN

MASPGNQNQQLGGGPFDVQRLFNPSSSPPPITTNPNTTFQNPNIPYPPPSSAASYPPPTVTGALYSYSPQTNPIYHPQFHIPSPPFQPDNPMPSSNLQHQRSVPYPTPPLQPPSPNSNPNPNHGARLMALLSAPPPTTVDNSSQSSIPMPQPTNPMNPSSLVPTWHSGSGSLQVPSSKLPKGRHLSGDRVSYDIDARLPGEVQPQLEVTPITKYGSDPGLVVGRQIAVNKAYICYGLKLGAIRVLNIHTALRSLLKGLSQ...

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_016122`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_016122

Location Chr03:111296753-111301351 (-)

Description Similar to VCR: Varicose-related protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g13290`	As a component of the decapping complex, may play a role in the degradation of mRNAs.	No verified direct reference in this release
`At3g13300`	As a component of the decapping complex, involved in the degradation of mRNAs.	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_016122 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Biological Process

GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006402 mRNA catabolic process Biological Process

GO:0007186 G protein-coupled receptor signaling pathway Biological Process

GO:0009791 post-embryonic development Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010071 root meristem specification Biological Process

GO:0010072 primary shoot apical meristem specification Biological Process

GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA Biological Process

GO:0071365 cellular response to auxin stimulus Biological Process

GO:0000932 P-body Cellular Component

KEGG gene cross-reference

ath:AT3G13290

ath:AT3G13300

hsa:23644

mmu:234699

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.

Cytoplasm0.613

Rank 1 · LXL04_016122 · OH-1004

Nucleus0.225

Rank 2 · LXL04_016122 · OH-1004

Golgi apparatus0.183

Rank 3 · LXL04_016122 · OH-1004

Lysosome / Vacuole0.109

Rank 4 · LXL04_016122 · OH-1004

Cell membrane0.107

Rank 5 · LXL04_016122 · 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.

PF16529.12Ge1_WD40208-521 aa

PF24817.2WD40_WDHD1_1st240-343 aa

PF24807.2WD40_CDC20-Fz371-460 aa

PF25175.2Beta-prop_WDR5372-458 aa

PF25173.2Beta-prop_WDR3_1st376-455 aa

PF21289.4EDC4_C1140-1245 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016122	`PF16529.12`	Ge1_WD40	208	521	7e-19	68.7
LXL04_016122	`PF24817.2`	WD40_WDHD1_1st	240	343	1e-10	42.0
LXL04_016122	`PF24807.2`	WD40_CDC20-Fz	371	460	1.9e-10	41.3
LXL04_016122	`PF25175.2`	Beta-prop_WDR5	372	458	9e-10	39.0
LXL04_016122	`PF25173.2`	Beta-prop_WDR3_1st	376	455	4.2e-10	40.4
LXL04_016122	`PF21289.4`	EDC4_C	1140	1245	9.1e-19	68.1

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
`Q9LTT9`	Arabidopsis thaliana	Varicose-related protein	50.719%	Swiss-Prot	strong database homology
`Q9LTT8`	Arabidopsis thaliana	Enhancer of mRNA-decapping protein 4	50.685%	Swiss-Prot	strong database homology

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