LXL04_032269 | RubberDandelionOmics

Gene overview

LXL04_032269

Reference: OH-1004 Chr: Chr07 Coordinates: 19725938-19728118 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1095 bp · LXL04_032269|LXL04_032269|OH1004|cDNA

ATGGAAGCCTCCTTGCCCAATGTCGACGACCGCAACAGCAGGCCTCAGATGGAAGTGAGCGAACCACCGATTATTAACGAACCACCGATTATTAATGTTGATGAACCACCGGTTGTTGATGTTGATGatggagatgatgaagaagTTGCTGATAATAAGTGTGGCGGTCAAAGTATCTTGGAAGCGCATCAGTCTCACAAGGCTAGCAGTTCAAATTCTGAGATTTACCACACCGTCGATGACTTATACTTCTGCGCTCT...

CDS

Download CDS FASTA

1095 bp · LXL04_032269|LXL04_032269|OH1004|CDS

ATGGAAGCCTCCTTGCCCAATGTCGACGACCGCAACAGCAGGCCTCAGATGGAAGTGAGCGAACCACCGATTATTAACGAACCACCGATTATTAATGTTGATGAACCACCGGTTGTTGATGTTGATGATGGAGATGATGAAGAAGTTGCTGATAATAAGTGTGGCGGTCAAAGTATCTTGGAAGCGCATCAGTCTCACAAGGCTAGCAGTTCAAATTCTGAGATTTACCACACCGTCGATGACTTATACTTCTGCGCTCT...

Protein

Download Protein FASTA

364 aa · LXL04_032269|LXL04_032269|OH1004|PROTEIN

MEASLPNVDDRNSRPQMEVSEPPIINEPPIINVDEPPVVDVDDGDDEEVADNKCGGQSILEAHQSHKASSSNSEIYHTVDDLYFCALHDNDEIFPISDEKYAEELQLQEALMSSASLTITSFKQDPSSSFPSTSTSTPPHTMNTKQPLLPPQLSVSFCHICMDSKPQSEMFSNTTVCRHLFCSDCIRGHVSAKIQENIAMVRCPDPKCKGVIGPEHCQSIVPKEVIERWEDALCESLIVGTQKFYCPFKDCLAMLVDDGG...

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_032269`
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_032269

Location Chr07:19725938-19728118 (+)

Description Similar to rnf144aa: Probable E3 ubiquitin-protein ligase RNF144A-A

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032269 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination Biological Process

GO:0002221 pattern recognition receptor signaling pathway Biological Process

GO:0002753 cytoplasmic pattern recognition receptor signaling pathway 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:0085020 protein K6-linked ubiquitination Biological Process

KEGG gene cross-reference

ath:AT2G26130

ddi:DDB_G0286961

dre:570968

hsa:9781

mmu:108089

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.

Nucleus0.862

Rank 1 · LXL04_032269 · OH-1004

Cytoplasm0.248

Rank 2 · LXL04_032269 · OH-1004

Cell membrane0.037

Rank 3 · LXL04_032269 · OH-1004

Endoplasmic reticulum0.029

Rank 4 · LXL04_032269 · OH-1004

Mitochondrion0.012

Rank 5 · LXL04_032269 · 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.

PF01485.28IBR227-289 aa

PF01485.28IBR310-357 aa

PF26200.2Rcat_RNF216316-354 aa

PF22191.3IBR_1317-353 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032269	`PF01485.28`	IBR	227	289	3.8e-18	66.0
LXL04_032269	`PF01485.28`	IBR	310	357	3.8e-18	66.0
LXL04_032269	`PF26200.2`	Rcat_RNF216	316	354	2.3e-06	28.8
LXL04_032269	`PF22191.3`	IBR_1	317	353	1.6e-08	35.0

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	30.808%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card