LXL04_005198 | RubberDandelionOmics

Gene overview

LXL04_005198

Reference: OH-1004 Chr: Chr01 Coordinates: 157614920-157616823 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1692 bp · LXL04_005198|LXL04_005198|OH1004|cDNA

ATGGACGAGGGCAGAGAGGAGCTGAGCAGAATCGCCGAGGCACAGCACCGGGAGGTAACGGCGGCCCGAGCCTTGGCGTCTGACCTAGACCTAGCATTCCGCCTCCAACTTGAAGAAGCCATGGTTGCCTCTCTCGCGTTTCAGCCCTCCTCCTCATCCACTCCACCAACGGAATCTCAACAGCCACCAGTCCTGGTCTCTAACGATGACGAAGTAAACCTGACCGACCTCCAAACCCTAGAGCTTGACGATTTTGAGGC...

CDS

Download CDS FASTA

1692 bp · LXL04_005198|LXL04_005198|OH1004|CDS

ATGGACGAGGGCAGAGAGGAGCTGAGCAGAATCGCCGAGGCACAGCACCGGGAGGTAACGGCGGCCCGAGCCTTGGCGTCTGACCTAGACCTAGCATTCCGCCTCCAACTTGAAGAAGCCATGGTTGCCTCTCTCGCGTTTCAGCCCTCCTCCTCATCCACTCCACCAACGGAATCTCAACAGCCACCAGTCCTGGTCTCTAACGATGACGAAGTAAACCTGACCGACCTCCAAACCCTAGAGCTTGACGATTTTGAGGC...

Protein

Download Protein FASTA

563 aa · LXL04_005198|LXL04_005198|OH1004|PROTEIN

MDEGREELSRIAEAQHREVTAARALASDLDLAFRLQLEEAMVASLAFQPSSSSTPPTESQQPPVLVSNDDEVNLTDLQTLELDDFEAEIRDHVVIETEKKKLQVDLHRRINDREMALTIHSMRDDRWEAEGDNYERPYGEGSSSSKREETSEVFRVYFKGMLSEERVRSTNSSQKTMTFAGIGVAICDSSDSIIFEMRKPLDLIDDDRISRRNVEGKSLIEALNAATALDLKRIEFYCDNYTLYQYVSGRWQPKQAKIKQ...

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_005198`
TK1151 ID	TkA01G076710
OH-1004 ID	LXL04_005198
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

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_005198

Location Chr01:157614920-157616823 (-)

Description Similar to At5g10370: ATP-dependent RNA helicase DEAH12, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g26130`	Acts as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.	A forward genetic approach in Arabidopsis thaliana identifies a RING-type ubiquitin ligase as a novel determinant of seed longevity.2014 · DOI: 10.1016/j.plantsci.2013.11.004
`At5g10370`	ATP-dependent RNA helicase DEAH12, chloroplastic.	No verified direct reference in this release
`At4g01020`	ATP-dependent RNA helicase DEAH11, chloroplastic.	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_005198 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006605 protein targeting Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010431 seed maturation Biological Process

GO:0010476 gibberellin mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0030435 sporulation resulting in formation of a cellular spore Biological Process

GO:0140547 acquisition of seed longevity Biological Process

GO:0000151 ubiquitin ligase complex Cellular Component

KEGG gene cross-reference

ath:AT2G26130

ath:AT4G01020

ath:AT5G10370

ddi:DDB_G0286961

xtr:100144731

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.

Nucleus0.596

Rank 1 · LXL04_005198 · OH-1004

Cytoplasm0.405

Rank 2 · LXL04_005198 · OH-1004

Cell membrane0.079

Rank 3 · LXL04_005198 · OH-1004

Endoplasmic reticulum0.052

Rank 4 · LXL04_005198 · OH-1004

Lysosome / Vacuole0.024

Rank 5 · LXL04_005198 · 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.

PF13456.13RVT_3177-295 aa

PF01485.28IBR395-450 aa

PF01485.28IBR470-518 aa

PF22191.3IBR_1478-515 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005198	`PF13456.13`	RVT_3	177	295	4.5e-19	69.3
LXL04_005198	`PF01485.28`	IBR	395	450	2.9e-17	63.2
LXL04_005198	`PF01485.28`	IBR	470	518	2.9e-17	63.2
LXL04_005198	`PF22191.3`	IBR_1	478	515	5.8e-08	33.2

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
`F4ITM1`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RSL1	38.781%	Swiss-Prot	moderate database homology
`F4KGU4`	Arabidopsis thaliana	ATP-dependent RNA helicase DEAH12, chloroplastic	25.448%	Swiss-Prot	weak database homology
`P0CE10`	Arabidopsis thaliana	ATP-dependent RNA helicase DEAH11, chloroplastic	24.373%	Swiss-Prot	weak database homology

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