LXL04_005197 | RubberDandelionOmics

Gene overview

LXL04_005197

Reference: OH-1004 Chr: Chr01 Coordinates: 157558701-157563454 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3192 bp · LXL04_005197|LXL04_005197|OH1004|cDNA

ATGGCGACGCCCGTCTCCCGCAAGAGAAAATTGGACGTCGAAGACGATGAACTTCTGATCCTCCTCTCCGAGCAACGCCGTGAACTGACTGCCGCTATCACTGCCGATTCCGACCTTGATTTCGCCTTCCAACTGCAAATGCAGGAAGCGATAAAAGTCTCTTTAACCTCTCAACCTTCTTCATCTTCGTCTTCCTCACACCAACCATTCCTCCTCCTTAACGAAGTCACAGACGCCCCTTCCGGCATCGCTCATCTCGT...

CDS

Download CDS FASTA

3192 bp · LXL04_005197|LXL04_005197|OH1004|CDS

ATGGCGACGCCCGTCTCCCGCAAGAGAAAATTGGACGTCGAAGACGATGAACTTCTGATCCTCCTCTCCGAGCAACGCCGTGAACTGACTGCCGCTATCACTGCCGATTCCGACCTTGATTTCGCCTTCCAACTGCAAATGCAGGAAGCGATAAAAGTCTCTTTAACCTCTCAACCTTCTTCATCTTCGTCTTCCTCACACCAACCATTCCTCCTCCTTAACGAAGTCACAGACGCCCCTTCCGGCATCGCTCATCTCGT...

Protein

Download Protein FASTA

1063 aa · LXL04_005197|LXL04_005197|OH1004|PROTEIN

MATPVSRKRKLDVEDDELLILLSEQRRELTAAITADSDLDFAFQLQMQEAIKVSLTSQPSSSSSSSHQPFLLLNEVTDAPSGIAHLVAEEIDNFERERSDRAVVEAEARNVQENLNRLIHDQIFARQIKGVPDDEWRKAGDNFEKPYGLSPSSIDEAFRVYFKGLVSDETVMNAKMPFAGIGVAICDTNDCCVFELRKPYLLGGNEGEGDLVELKALIEALNTAVTLGLRRVHIFCDSNSSYQYLTGKGRPTNNSSLTLI...

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_005197`
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_005197

Location Chr01:157558701-157563454 (-)

Description Similar to rbrA: Probable E3 ubiquitin-protein ligase rbrA

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
`At4g01020`	ATP-dependent RNA helicase DEAH11, chloroplastic.	No verified direct reference in this release
`At2g31760`	Might act 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.	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_005197 · 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: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

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G26130

ath:AT4G01020

ddi:DDB_G0286961

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.

Cytoplasm0.620

Rank 1 · LXL04_005197 · OH-1004

Nucleus0.412

Rank 2 · LXL04_005197 · OH-1004

Cell membrane0.086

Rank 3 · LXL04_005197 · OH-1004

Endoplasmic reticulum0.050

Rank 4 · LXL04_005197 · OH-1004

Mitochondrion0.045

Rank 5 · LXL04_005197 · 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.

PF13456.13RVT_3175-293 aa

PF01485.28IBR395-451 aa

PF01485.28IBR466-519 aa

PF22191.3IBR_1478-516 aa

PF13456.13RVT_3704-826 aa

PF01485.28IBR928-987 aa

PF01485.28IBR998-1050 aa

PF22191.3IBR_11009-1047 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005197	`PF13456.13`	RVT_3	175	293	4.4e-32	111.3
LXL04_005197	`PF01485.28`	IBR	395	451	1e-27	96.7
LXL04_005197	`PF01485.28`	IBR	466	519	1e-27	96.7
LXL04_005197	`PF22191.3`	IBR_1	478	516	1.1e-11	45.2
LXL04_005197	`PF13456.13`	RVT_3	704	826	4.4e-32	111.3
LXL04_005197	`PF01485.28`	IBR	928	987	1e-27	96.7
LXL04_005197	`PF01485.28`	IBR	998	1050	1e-27	96.7
LXL04_005197	`PF22191.3`	IBR_1	1009	1047	1.1e-11	45.2

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	36.695%	Swiss-Prot	weak database homology
`P0CE10`	Arabidopsis thaliana	ATP-dependent RNA helicase DEAH11, chloroplastic	25.500%	Swiss-Prot	weak database homology
`Q9SKC4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI10	28.372%	Swiss-Prot	weak database homology

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