LXL04_026346 | RubberDandelionOmics

Gene overview

LXL04_026346

Reference: OH-1004 Chr: Chr05 Coordinates: 124996933-124998471 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1122 bp · LXL04_026346|LXL04_026346|OH1004|cDNA

ATGTTCTTTATGATGCAAAAGCGACCACACATGGAGAAGATAACTTTACCGCTcttcttctatttcttcttgTTCAAATCCATCTCCGGCGCCGATGACTGCCTCCCCGCCGCCTGCAGCCCCACCGGACCTCAGGTACGTTTCCCATTTCGTATCCGGGGTAAGCAACCATCCCACTGCGGATTCCCTGGTTTCGATCTCTCATGCAATAAACGAAATCGAACAATTCTACACCTTTCCTCCTCCCGATCATACATCGT...

CDS

Download CDS FASTA

1122 bp · LXL04_026346|LXL04_026346|OH1004|CDS

ATGTTCTTTATGATGCAAAAGCGACCACACATGGAGAAGATAACTTTACCGCTCTTCTTCTATTTCTTCTTGTTCAAATCCATCTCCGGCGCCGATGACTGCCTCCCCGCCGCCTGCAGCCCCACCGGACCTCAGGTACGTTTCCCATTTCGTATCCGGGGTAAGCAACCATCCCACTGCGGATTCCCTGGTTTCGATCTCTCATGCAATAAACGAAATCGAACAATTCTACACCTTTCCTCCTCCCGATCATACATCGT...

Protein

Download Protein FASTA

373 aa · LXL04_026346|LXL04_026346|OH1004|PROTEIN

MFFMMQKRPHMEKITLPLFFYFFLFKSISGADDCLPAACSPTGPQVRFPFRIRGKQPSHCGFPGFDLSCNKRNRTILHLSSSRSYIVNRISYGAQIIYIDPEFCRPKRIVSFRLTGTPFDFSSVRGYKFYNCSVQKSNYMFPAETLPCLDSVNHSVIAVRTGLIPEGEPPENCQDIALISVPIRWYGSMKEELELMWFTPFCRPCEIEGRMCGLKNGDGETTCFGSPVGIQRNAKYALSIGTGVSILICIFGIVSYTAHK...

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_026346`
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_026346

Location Chr05:124996933-124998471 (+)

Description Similar to ATL22: RING-H2 finger protein ATL22

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g25410`	RING-H2 finger protein ATL22.	No verified direct reference in this release
`At2g46494`	Putative RING-H2 finger protein ATL21B.	No verified direct reference in this release
`At2g46495`	Putative RING-H2 finger protein ATL21A.	No verified direct reference in this release
`At1g28040`	RING-H2 finger protein ATL20.	No verified direct reference in this release
`At2g46493`	Putative RING-H2 finger protein ATL21C.	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_026346 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0030247 polysaccharide binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G28040

ath:AT2G25410

ath:AT2G46493

ath:AT2G46494

ath:AT2G46495

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.

Cell membrane0.750

Rank 1 · LXL04_026346 · OH-1004

Endoplasmic reticulum0.107

Rank 2 · LXL04_026346 · OH-1004

Cytoplasm0.100

Rank 3 · LXL04_026346 · OH-1004

Nucleus0.085

Rank 4 · LXL04_026346 · OH-1004

Extracellular0.052

Rank 5 · LXL04_026346 · 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.

PF13947.12GUB_WAK_bind34-99 aa

PF12678.14zf-rbx1306-357 aa

PF13639.13zf-RING_2313-357 aa

PF17123.12zf-RING_11315-343 aa

PF13923.13zf-C3HC4_2315-356 aa

PF00097.32zf-C3HC4315-356 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026346	`PF13947.12`	GUB_WAK_bind	34	99	2.4e-17	63.8
LXL04_026346	`PF12678.14`	zf-rbx1	306	357	4.4e-11	43.6
LXL04_026346	`PF13639.13`	zf-RING_2	313	357	3.8e-14	53.4
LXL04_026346	`PF17123.12`	zf-RING_11	315	343	3.4e-09	36.9
LXL04_026346	`PF13923.13`	zf-C3HC4_2	315	356	6.2e-08	33.0
LXL04_026346	`PF00097.32`	zf-C3HC4	315	356	2.5e-07	31.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SKK8`	Arabidopsis thaliana	RING-H2 finger protein ATL22	34.097%	Swiss-Prot	moderate database homology
`P0CH02`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL21B	34.808%	Swiss-Prot	moderate database homology
`P0CH01`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL21A	33.239%	Swiss-Prot	moderate database homology
`Q9C7E9`	Arabidopsis thaliana	RING-H2 finger protein ATL20	33.550%	Swiss-Prot	moderate database homology
`P0CH03`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL21C	31.778%	Swiss-Prot	moderate database homology

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