LXL04_032268 | RubberDandelionOmics

Gene overview

LXL04_032268

Reference: OH-1004 Chr: Chr07 Coordinates: 19608824-19609953 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1038 bp · LXL04_032268|LXL04_032268|OH1004|cDNA

ATGGATGCATCTTCATCATCACAAGATGATgcatcatcttcatcatcccAAGATGATGCATCATCGTCCTCATCACAAGATGATGCATCATCTTCATCATTCCAAGATGATGCATCATCGTCATCATCATCCCAGATGgactcatcatcatcatccgaAGATGATGCATCACCGTCGTCATCATCCCAAAATGATGCATCATTTTCATCACCCAAGTATAATGCATCATCTTCGTCATCCGAAGATGATAcatcatcatc...

CDS

Download CDS FASTA

1038 bp · LXL04_032268|LXL04_032268|OH1004|CDS

ATGGATGCATCTTCATCATCACAAGATGATGCATCATCTTCATCATCCCAAGATGATGCATCATCGTCCTCATCACAAGATGATGCATCATCTTCATCATTCCAAGATGATGCATCATCGTCATCATCATCCCAGATGGACTCATCATCATCATCCGAAGATGATGCATCACCGTCGTCATCATCCCAAAATGATGCATCATTTTCATCACCCAAGTATAATGCATCATCTTCGTCATCCGAAGATGATACATCATCATC...

Protein

Download Protein FASTA

345 aa · LXL04_032268|LXL04_032268|OH1004|PROTEIN

MDASSSSQDDASSSSSQDDASSSSSQDDASSSSFQDDASSSSSSQMDSSSSSEDDASPSSSSQNDASFSSPKYNASSSSSEDDTSSSTSLSLSSFPSTASPWGPLKRKQPMATSTSWHAPKRNQPMVASKAFQSSDTFCNICIETKSKSDMFLNTTICSHVYCSDCICKHISAKIKDNITKVKCPHPECNGEIGPEHCRTIIPKEVLERWEDALCESLILGTQKIYCPFKDCSAMLVDDGGKAVTSSECPNCNRLFCAQC...

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_032268`
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_032268

Location Chr07:19608824-19609953 (+)

Description Similar to ARI9: Probable E3 ubiquitin-protein ligase ARI9

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
`At2g31770`	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
`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_032268 · 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:0085020 protein K6-linked ubiquitination Biological Process

GO:0140547 acquisition of seed longevity Biological Process

KEGG gene cross-reference

ath:AT2G26130

ath:AT2G31760

ath:AT2G31770

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.

Nucleus0.878

Rank 1 · LXL04_032268 · OH-1004

Cytoplasm0.227

Rank 2 · LXL04_032268 · OH-1004

Cell membrane0.034

Rank 3 · LXL04_032268 · OH-1004

Endoplasmic reticulum0.027

Rank 4 · LXL04_032268 · OH-1004

Mitochondrion0.013

Rank 5 · LXL04_032268 · 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.

PF01485.28IBR208-270 aa

PF01485.28IBR290-338 aa

PF22191.3IBR_1296-335 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032268	`PF01485.28`	IBR	208	270	3.6e-20	72.5
LXL04_032268	`PF01485.28`	IBR	290	338	3.6e-20	72.5
LXL04_032268	`PF22191.3`	IBR_1	296	335	1.7e-06	28.5

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	31.633%	Swiss-Prot	moderate database homology
`Q9SKC3`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI9	32.110%	Swiss-Prot	moderate database homology
`Q9SKC4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase ARI10	29.911%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card