LXL04_027952 | RubberDandelionOmics

Gene overview

LXL04_027952

Reference: OH-1004 Chr: Chr06 Coordinates: 27537654-27538739 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1086 bp · LXL04_027952|LXL04_027952|OH1004|cDNA

ATGAACTTTCCGACAACTCGCCAGCCGGAGTTCATCAGAATTCCGACGAACCCACAAAAGCTACTTACTTTTCTCATAACCTTTCTCATACTATTCCCAAATTCAACACTTTCACAATCATCATACACCTCTGCAATCGATGAAAACCATTCAAATTCATCTGATTCCGCCACTAAATTCCAGCCAAGTTTAGCTGTCGTCATCGGAGTTCTCTCAATCGTCTTCTCATTAACATCTTTAGTCTTAATTTACGCAAAATG...

CDS

Download CDS FASTA

1086 bp · LXL04_027952|LXL04_027952|OH1004|CDS

ATGAACTTTCCGACAACTCGCCAGCCGGAGTTCATCAGAATTCCGACGAACCCACAAAAGCTACTTACTTTTCTCATAACCTTTCTCATACTATTCCCAAATTCAACACTTTCACAATCATCATACACCTCTGCAATCGATGAAAACCATTCAAATTCATCTGATTCCGCCACTAAATTCCAGCCAAGTTTAGCTGTCGTCATCGGAGTTCTCTCAATCGTCTTCTCATTAACATCTTTAGTCTTAATTTACGCAAAATG...

Protein

Download Protein FASTA

361 aa · LXL04_027952|LXL04_027952|OH1004|PROTEIN

MNFPTTRQPEFIRIPTNPQKLLTFLITFLILFPNSTLSQSSYTSAIDENHSNSSDSATKFQPSLAVVIGVLSIVFSLTSLVLIYAKCCHVSSSVHHESFGNLPRTRSRFSGIDQTIIDSLPFFTFSTLKGSRNGLECSVCLSAFEDVEVLRLLPKCKHAFHIDCIDQWLRKHSSCPLCRIKVIVDDITLFTYSNSLRFHEPDPSSLGLFIEREGSSRFLKNEEILDKFNHRIMVCDDNDPMIIKNRWSNVSSSDLLFLKS...

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_027952`
TK1151 ID	TkA07G108590
OH-1004 ID	LXL04_027952
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

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_027952

Location Chr06:27537654-27538739 (+)

Description Similar to ATL12: Putative RING-H2 finger protein ATL12

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g20030`	Putative RING-H2 finger protein ATL12.	No verified direct reference in this release
`At4g28890`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	No verified direct reference in this release
`At5g05810`	RING-H2 finger protein ATL43.	No verified direct reference in this release
`At1g72200`	RING-H2 finger protein ATL11.	No verified direct reference in this release
`At4g40070`	RING-H2 finger protein ATL32.	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_027952 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion 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:AT1G72200

ath:AT2G20030

ath:AT4G28890

ath:AT4G40070

ath:AT5G05810

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.

Nucleus0.345

Rank 1 · LXL04_027952 · OH-1004

Cell membrane0.311

Rank 2 · LXL04_027952 · OH-1004

Cytoplasm0.274

Rank 3 · LXL04_027952 · OH-1004

Endoplasmic reticulum0.131

Rank 4 · LXL04_027952 · OH-1004

Lysosome / Vacuole0.077

Rank 5 · LXL04_027952 · 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_2136-179 aa

PF17123.12zf-RING_11136-165 aa

PF13923.13zf-C3HC4_2136-178 aa

PF00097.32zf-C3HC4137-178 aa

PF13445.13zf-RING_UBOX137-176 aa

PF12861.14zf-ANAPC11140-183 aa

PF12678.14zf-rbx1149-179 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027952	`PF13639.13`	zf-RING_2	136	179	7.7e-14	52.4
LXL04_027952	`PF17123.12`	zf-RING_11	136	165	2.1e-09	37.6
LXL04_027952	`PF13923.13`	zf-C3HC4_2	136	178	2.1e-09	37.7
LXL04_027952	`PF00097.32`	zf-C3HC4	137	178	3.6e-08	33.8
LXL04_027952	`PF13445.13`	zf-RING_UBOX	137	176	1e-05	26.1
LXL04_027952	`PF12861.14`	zf-ANAPC11	140	183	2.2e-06	28.4
LXL04_027952	`PF12678.14`	zf-rbx1	149	179	1e-09	39.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9SL78`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL12	43.386%	Swiss-Prot	moderate database homology
`Q5XF85`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL42	39.320%	Swiss-Prot	moderate database homology
`Q5EAE9`	Arabidopsis thaliana	RING-H2 finger protein ATL43	44.910%	Swiss-Prot	weak database homology
`Q84W40`	Arabidopsis thaliana	RING-H2 finger protein ATL11	41.958%	Swiss-Prot	weak database homology
`Q8W571`	Arabidopsis thaliana	RING-H2 finger protein ATL32	42.105%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card