LXL04_015347 | RubberDandelionOmics

Gene overview

LXL04_015347

Reference: OH-1004 Chr: Chr03 Coordinates: 69137009-69143259 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4755 bp · LXL04_015347|LXL04_015347|OH1004|cDNA

ATGGAAGTTCAAATGTGCTTCGACTGTCTTCAACGTCAACTTCGAACCGATTTCTCCGACAAACTACTTTTCAATTATGCCCTCGCCGCTTCCGCCCTTCCGTTCGCCTCCGACGCTGTTGTTCAGGTTCTAAAATCTGATGGGGAAGTTTCACCTCACTTCATATTGATGTATTTGCCGATTAATGAAGATGATTGCTTCACCAATTACATTAATGAGCATTGTCCAGAAACGCCAACTGTCAATGATCATAAAACAAC...

CDS

Download CDS FASTA

4755 bp · LXL04_015347|LXL04_015347|OH1004|CDS

ATGGAAGTTCAAATGTGCTTCGACTGTCTTCAACGTCAACTTCGAACCGATTTCTCCGACAAACTACTTTTCAATTATGCCCTCGCCGCTTCCGCCCTTCCGTTCGCCTCCGACGCTGTTGTTCAGGTTCTAAAATCTGATGGGGAAGTTTCACCTCACTTCATATTGATGTATTTGCCGATTAATGAAGATGATTGCTTCACCAATTACATTAATGAGCATTGTCCAGAAACGCCAACTGTCAATGATCATAAAACAAC...

Protein

Download Protein FASTA

1584 aa · LXL04_015347|LXL04_015347|OH1004|PROTEIN

MEVQMCFDCLQRQLRTDFSDKLLFNYALAASALPFASDAVVQVLKSDGEVSPHFILMYLPINEDDCFTNYINEHCPETPTVNDHKTTDNTPSSALPQDNQEVTTGNLHDKPSTPLQTKPKEPQFLPNGGVKTSLPGLKCNNSTCYFSKSFSCLRTLTSLVPISQIGPTSYSDLEELALSFSSGTTEDHLLHSLTLLIQGKPTGKDTINFLDLIGIPSFTKTTFPGCIRHPNIVPILSIMKSSNSTHINLIFPKTPYTLEN...

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_015347`
TK1151 ID	TkA02G345330
OH-1004 ID	LXL04_015347
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	98.500
Protein coverage (%)	TK1151 100.000 / OH-1004 77.083 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_015347

Location Chr03:69137009-69143259 (-)

Description Similar to GFS12: Protein GFS12

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g18525`	May act predominantly to suppress BCHC1, which itself is a negative factor in protein storage vacuole (PSV) trafficking regulation and plant effector triggered immunity (ETI).	BEACH-domain proteins act together in a cascade to mediate vacuolar protein trafficking and disease resistance in Arabidopsis.2015 · DOI: 10.1016/j.molp.2014.11.015

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_015347 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006623 protein targeting to vacuole Biological Process

GO:0035973 aggrephagy Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0045022 early endosome to late endosome transport Biological Process

GO:2000643 positive regulation of early endosome to late endosome transport Biological Process

GO:0000421 autophagosome membrane Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005765 lysosomal membrane Cellular Component

GO:0005769 early endosome Cellular Component

GO:0005770 late endosome Cellular Component

KEGG gene cross-reference

ath:AT5G18525

ddi:DDB_G0268088

dre:100333062

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.

Cytoplasm0.539

Rank 1 · LXL04_015347 · OH-1004

Nucleus0.280

Rank 2 · LXL04_015347 · OH-1004

Golgi apparatus0.138

Rank 3 · LXL04_015347 · OH-1004

Cell membrane0.096

Rank 4 · LXL04_015347 · OH-1004

Lysosome / Vacuole0.088

Rank 5 · LXL04_015347 · 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.

PF00069.32Pkinase227-308 aa

PF02138.24Beach358-567 aa

PF00069.32Pkinase697-771 aa

PF24814.2WD40_Prp191259-1494 aa

PF25171.2Beta-prop_WDR36-Utp21_1st1294-1512 aa

PF24807.2WD40_CDC20-Fz1363-1510 aa

PF24817.2WD40_WDHD1_1st1383-1494 aa

PF25174.2Beta-prop_THOC31384-1495 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015347	`PF00069.32`	Pkinase	227	308	6.2e-15	56.0
LXL04_015347	`PF02138.24`	Beach	358	567	3.7e-40	138.8
LXL04_015347	`PF00069.32`	Pkinase	697	771	6.2e-15	56.0
LXL04_015347	`PF24814.2`	WD40_Prp19	1259	1494	6.9e-17	62.1
LXL04_015347	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	1294	1512	4.6e-12	46.7
LXL04_015347	`PF24807.2`	WD40_CDC20-Fz	1363	1510	2.5e-12	47.4
LXL04_015347	`PF24817.2`	WD40_WDHD1_1st	1383	1494	5.6e-09	36.3
LXL04_015347	`PF25174.2`	Beta-prop_THOC3	1384	1495	8.4e-10	38.8
LXL04_015347	`PF24796.2`	WDR55	1384	1494	1.3e-08	34.9
LXL04_015347	`PF25173.2`	Beta-prop_WDR3_1st	1394	1523	2.6e-14	54.1
LXL04_015347	`PF25391.2`	WD40_Gbeta	1397	1517	9.6e-07	28.8
LXL04_015347	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	1399	1493	2.6e-06	27.7
LXL04_015347	`PF25172.2`	Beta-prop_WDR3_2nd	1403	1492	1.3e-08	35.2
LXL04_015347	`PF24814.2`	WD40_Prp19	1422	1542	6.9e-17	62.1
LXL04_015347	`PF25047.1`	Beta-prop_TEP1_2nd	1422	1525	4.3e-09	36.6
LXL04_015347	`PF23381.2`	Beta-prop_IFT122_1st	1430	1534	4.7e-11	43.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`F4JY12`	Arabidopsis thaliana	Protein GFS12	51.619%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card