LXL04_007555 | RubberDandelionOmics

Gene overview

LXL04_007555

Reference: OH-1004 Chr: Chr02 Coordinates: 51937382-51938035 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

654 bp · LXL04_007555|LXL04_007555|OH1004|cDNA

ATGTCAAGCCTATCTACTGAGCTCTTTCAAGATGAATTGAGGCATTTCAATTCAAGAAAGCTTTTACTTCACAATTATTCATACCAACAACCCGTGATAGCTCCCTCACCATCAACCCCATATCTAGAACATAGCAACTTTGACGCGAATGTGGTGATGGTGCTTTCGGTACTTCTATGTGCTCTAATTTGCTCACTAGGGTTGAACTCCATCATCAGATGTGTTTTAAGATGCTCATCCTTGGTTGGCTCACAAAGCAG...

CDS

Download CDS FASTA

654 bp · LXL04_007555|LXL04_007555|OH1004|CDS

ATGTCAAGCCTATCTACTGAGCTCTTTCAAGATGAATTGAGGCATTTCAATTCAAGAAAGCTTTTACTTCACAATTATTCATACCAACAACCCGTGATAGCTCCCTCACCATCAACCCCATATCTAGAACATAGCAACTTTGACGCGAATGTGGTGATGGTGCTTTCGGTACTTCTATGTGCTCTAATTTGCTCACTAGGGTTGAACTCCATCATCAGATGTGTTTTAAGATGCTCATCCTTGGTTGGCTCACAAAGCAG...

Protein

Download Protein FASTA

217 aa · LXL04_007555|LXL04_007555|OH1004|PROTEIN

MSSLSTELFQDELRHFNSRKLLLHNYSYQQPVIAPSPSTPYLEHSNFDANVVMVLSVLLCALICSLGLNSIIRCVLRCSSLVGSQSSDNQESTSAKLATTGIKKKALKTFPTVSYSEGLKLPGLDKECVICLGDFATGERVKILPKCNHGFHVKCIDKWLSSHSSCPTCRHSLLDTCQKIVTGGYYSSTTSSQGPSTTPVLNIVPLQHEGLLRNYET

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_007555`
TK1151 ID	TkA03G189980
OH-1004 ID	LXL04_007555
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	73.800
Protein coverage (%)	TK1151 99.355 / OH-1004 75.576 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_007555

Location Chr02:51937382-51938035 (+)

Description Similar to ATL78: RING-H2 finger protein ATL78

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g49230`	RING-H2 finger protein ATL78.	No verified direct reference in this release
`At1g49220`	RING-H2 finger protein ATL10.	No verified direct reference in this release
`At1g49200`	RING-H2 finger protein ATL75.	No verified direct reference in this release
`At1g49210`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	No verified direct reference in this release
`At3g18773`	RING-H2 finger protein ATL77.	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_007555 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G49200

ath:AT1G49210

ath:AT1G49220

ath:AT1G49230

ath:AT3G18773

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 / Vacuole0.317

Rank 1 · LXL04_007555 · OH-1004

Cell membrane0.290

Rank 2 · LXL04_007555 · OH-1004

Endoplasmic reticulum0.246

Rank 3 · LXL04_007555 · OH-1004

Cytoplasm0.172

Rank 4 · LXL04_007555 · OH-1004

Nucleus0.133

Rank 5 · LXL04_007555 · 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.

PF13639.13zf-RING_2127-170 aa

PF17123.12zf-RING_11127-156 aa

PF13923.13zf-C3HC4_2127-169 aa

PF12678.14zf-rbx1128-170 aa

PF00097.32zf-C3HC4128-169 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007555	`PF13639.13`	zf-RING_2	127	170	2.7e-15	57.1
LXL04_007555	`PF17123.12`	zf-RING_11	127	156	1.1e-11	44.9
LXL04_007555	`PF13923.13`	zf-C3HC4_2	127	169	7.1e-10	39.3
LXL04_007555	`PF12678.14`	zf-rbx1	128	170	6.9e-10	39.7
LXL04_007555	`PF00097.32`	zf-C3HC4	128	169	1.5e-06	28.7

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
`Q6NQG7`	Arabidopsis thaliana	RING-H2 finger protein ATL78	58.768%	Swiss-Prot	strong database homology
`P0C034`	Arabidopsis thaliana	RING-H2 finger protein ATL10	48.058%	Swiss-Prot	moderate database homology
`Q94BY6`	Arabidopsis thaliana	RING-H2 finger protein ATL75	46.948%	Swiss-Prot	moderate database homology
`Q6NML0`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL76	46.829%	Swiss-Prot	moderate database homology
`Q9LS99`	Arabidopsis thaliana	RING-H2 finger protein ATL77	41.284%	Swiss-Prot	moderate database homology

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