LXL04_012421 | RubberDandelionOmics

Gene overview

LXL04_012421

Reference: OH-1004 Chr: Chr03 Coordinates: 12104498-12104989 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

492 bp · LXL04_012421|LXL04_012421|OH1004|cDNA

ATGGAAGACAACTCAGTGACACTCAAATTGATCTCCCTTTTGGTCATCGTTTCATTCGTAGCCATCTTAGTCGCCATCTACCACTTTGTCACTGTTAGTTGGTGCTATCGTCGGCGAAATAATTTCCCACCACACCATGTGCACCAACAAAATCATCATCTGGATCATACCGACTACAGTCTGGAGAATTCAGTGGTGTTGCTCATCCCGGCCCACAAGCACCAAAAAGGGTCGAAAGTAGGTACAAAAGAATGCGATGA...

CDS

Download CDS FASTA

492 bp · LXL04_012421|LXL04_012421|OH1004|CDS

ATGGAAGACAACTCAGTGACACTCAAATTGATCTCCCTTTTGGTCATCGTTTCATTCGTAGCCATCTTAGTCGCCATCTACCACTTTGTCACTGTTAGTTGGTGCTATCGTCGGCGAAATAATTTCCCACCACACCATGTGCACCAACAAAATCATCATCTGGATCATACCGACTACAGTCTGGAGAATTCAGTGGTGTTGCTCATCCCGGCCCACAAGCACCAAAAAGGGTCGAAAGTAGGTACAAAAGAATGCGATGA...

Protein

Download Protein FASTA

163 aa · LXL04_012421|LXL04_012421|OH1004|PROTEIN

MEDNSVTLKLISLLVIVSFVAILVAIYHFVTVSWCYRRRNNFPPHHVHQQNHHLDHTDYSLENSVVLLIPAHKHQKGSKVGTKECDDDAMCSICLCEFEENEELRTLPECSHSFHVPCIDMWLFSHSTCPVCRADAVPSSQILFQFLDSDSDIEIRQEVLNIV

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_012421`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_012421

Location Chr03:12104498-12104989 (-)

Description Similar to ATL51: RING-H2 finger protein ATL51

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g03550`	RING-H2 finger protein ATL51.	No verified direct reference in this release
`At5g17600`	RING-H2 finger protein ATL52.	No verified direct reference in this release
`At1g23980`	RING-H2 finger protein ATL47.	No verified direct reference in this release
`At4g40070`	RING-H2 finger protein ATL32.	No verified direct reference in this release
`At4g17905`	Putative RING-H2 finger protein ATL53.	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_012421 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G23980

ath:AT3G03550

ath:AT4G17905

ath:AT4G40070

ath:AT5G17600

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.

Lysosome / Vacuole0.336

Rank 1 · LXL04_012421 · OH-1004

Cytoplasm0.248

Rank 2 · LXL04_012421 · OH-1004

Cell membrane0.247

Rank 3 · LXL04_012421 · OH-1004

Endoplasmic reticulum0.214

Rank 4 · LXL04_012421 · OH-1004

Nucleus0.155

Rank 5 · LXL04_012421 · 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.

PF12678.14zf-rbx188-133 aa

PF13639.13zf-RING_290-133 aa

PF13923.13zf-C3HC4_290-132 aa

PF17123.12zf-RING_1191-119 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012421	`PF12678.14`	zf-rbx1	88	133	3.4e-07	31.1
LXL04_012421	`PF13639.13`	zf-RING_2	90	133	1.7e-13	51.3
LXL04_012421	`PF13923.13`	zf-C3HC4_2	90	132	6.9e-06	26.5
LXL04_012421	`PF17123.12`	zf-RING_11	91	119	2.6e-10	40.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SRQ8`	Arabidopsis thaliana	RING-H2 finger protein ATL51	37.107%	Swiss-Prot	moderate database homology
`Q9LF64`	Arabidopsis thaliana	RING-H2 finger protein ATL52	36.090%	Swiss-Prot	moderate database homology
`Q8GW38`	Arabidopsis thaliana	RING-H2 finger protein ATL47	31.293%	Swiss-Prot	moderate database homology
`Q8W571`	Arabidopsis thaliana	RING-H2 finger protein ATL32	35.075%	Swiss-Prot	moderate database homology
`P0C041`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL53	34.545%	Swiss-Prot	moderate database homology

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