LXL04_018667 | RubberDandelionOmics

Gene overview

LXL04_018667

Reference: OH-1004 Chr: Chr04 Coordinates: 16433246-16434565 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

723 bp · LXL04_018667|LXL04_018667|OH1004|cDNA

ATGAACAACACACAAGGTCAAACAATTATGTATGCAAGAGGTGGTAGGAGAAGAAAGATTCTTGATGTTGACCTCAATGACACTCCACCAATTGAAGACCATGACCACTTGGCAGCAAGTCTAGTTCTCTCTTTGACTTATGGTGGACAAGGTGTTGACCATGGTCAAGTGCCCCTCACTGCATCCACTCCAGTTACCCAACCTCTTCAACCACAACCTGTTCCTATCGATGTTGAGGAATTGGATGATGATGTCATCAT...

CDS

Download CDS FASTA

723 bp · LXL04_018667|LXL04_018667|OH1004|CDS

ATGAACAACACACAAGGTCAAACAATTATGTATGCAAGAGGTGGTAGGAGAAGAAAGATTCTTGATGTTGACCTCAATGACACTCCACCAATTGAAGACCATGACCACTTGGCAGCAAGTCTAGTTCTCTCTTTGACTTATGGTGGACAAGGTGTTGACCATGGTCAAGTGCCCCTCACTGCATCCACTCCAGTTACCCAACCTCTTCAACCACAACCTGTTCCTATCGATGTTGAGGAATTGGATGATGATGTCATCAT...

Protein

Download Protein FASTA

240 aa · LXL04_018667|LXL04_018667|OH1004|PROTEIN

MNNTQGQTIMYARGGRRRKILDVDLNDTPPIEDHDHLAASLVLSLTYGGQGVDHGQVPLTASTPVTQPLQPQPVPIDVEELDDDVIISSPRAFEQARNSSRRVSRRTSVIDVESGKHYMIFDKEVGRYGNNRNQRRRLHQQPQVLSDDSLYVILEGSGSSMDESEPSVTVVPPPPPPPEPPTFNCPVCMGPLVEEVTTKCGHIFCKGCIKAAIAAQSKCPTCRRKVTNRELIRIYLPSAS

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_018667`
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_018667

Location Chr04:16433246-16434565 (-)

Description Similar to RNF4: E3 ubiquitin-protein ligase RNF4

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g03510`	E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of aquaporin PIP2-1.	Rma1, a novel type of RING finger protein conserved from Arabidopsis to human, is a membrane-bound ubiquitin ligase.2001 · DOI: 10.1242/jcs.114.10.1949 Characterization of three Arabidopsis homologs of human RING membrane anchor E3 ubiquitin ligase.2009 · DOI: 10.1007/s00299-009-0680-8 Drought stress-induced Rma1H1, a RING membrane-anchor E3 ubiquitin ligase homolog, regulates aquaporin levels via ubiquitination in transgenic Arabidopsis plants.2009 · DOI: 10.1105/tpc.108.061994

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018667 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0030154 cell differentiation Biological Process

GO:0032355 response to estradiol Biological Process

GO:0032527 protein exit from endoplasmic reticulum Biological Process

GO:0036503 ERAD pathway Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0044752 response to human chorionic gonadotropin Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

KEGG gene cross-reference

ath:AT4G03510

hsa:6047

mmu:19822

mmu:67504

rno:29274

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.

Nucleus0.958

Rank 1 · LXL04_018667 · OH-1004

Cytoplasm0.188

Rank 2 · LXL04_018667 · OH-1004

Mitochondrion0.018

Rank 3 · LXL04_018667 · OH-1004

Cell membrane0.016

Rank 4 · LXL04_018667 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_018667 · 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.

PF13923.13zf-C3HC4_2184-222 aa

PF13639.13zf-RING_2184-223 aa

PF13920.13zf-C3HC4_3184-228 aa

PF14634.13zf-RING_5184-224 aa

PF00097.32zf-C3HC4185-222 aa

PF13445.13zf-RING_UBOX185-220 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018667	`PF13923.13`	zf-C3HC4_2	184	222	2.6e-10	40.6
LXL04_018667	`PF13639.13`	zf-RING_2	184	223	3e-09	37.7
LXL04_018667	`PF13920.13`	zf-C3HC4_3	184	228	6.8e-08	32.9
LXL04_018667	`PF14634.13`	zf-RING_5	184	224	1.2e-06	29.1
LXL04_018667	`PF00097.32`	zf-C3HC4	185	222	1.9e-09	38.0
LXL04_018667	`PF13445.13`	zf-RING_UBOX	185	220	8.3e-07	29.6

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
`O64425`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RMA1	30.476%	Swiss-Prot	weak database homology

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