LXL04_003511 | RubberDandelionOmics

Gene overview

LXL04_003511

Reference: OH-1004 Chr: Chr01 Coordinates: 81626454-81628780 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1617 bp · LXL04_003511|LXL04_003511|OH1004|cDNA

ATGTTCGATGCCAGATTCATCAATTGTCATTTAGCCCTCATACGGATGCAAAAGGAATCATGGAACGTAGTACTTGTACACGGTGAAAAACCGAAAATGGATTTGCTAAAAGCAAAAATTAAATCAGAATTAGGAATCGACTGTTTTGACCCCGCAAATACCGAAACCGTATCTTTTCCTTCAACCCGTTTTGAAAAGTCCGATGCTTCAAATGCATTTATCCGTAGTTCTTTGACTCCCAATTTCAAGTTCCCTAAAGA...

CDS

Download CDS FASTA

1617 bp · LXL04_003511|LXL04_003511|OH1004|CDS

ATGTTCGATGCCAGATTCATCAATTGTCATTTAGCCCTCATACGGATGCAAAAGGAATCATGGAACGTAGTACTTGTACACGGTGAAAAACCGAAAATGGATTTGCTAAAAGCAAAAATTAAATCAGAATTAGGAATCGACTGTTTTGACCCCGCAAATACCGAAACCGTATCTTTTCCTTCAACCCGTTTTGAAAAGTCCGATGCTTCAAATGCATTTATCCGTAGTTCTTTGACTCCCAATTTCAAGTTCCCTAAAGA...

Protein

Download Protein FASTA

538 aa · LXL04_003511|LXL04_003511|OH1004|PROTEIN

MFDARFINCHLALIRMQKESWNVVLVHGEKPKMDLLKAKIKSELGIDCFDPANTETVSFPSTRFEKSDASNAFIRSSLTPNFKFPKDEITDMPSLHVHDERVSEGILTRVDGKKLKVIHQDEVVTMVGGVKTEVEFCYCFGLKLCNLKSIRVFDSDDDGLIGALNLKLSDEFGDLGLRVCLEKGCVWPIKYRELITLFPSHLWKFQDAGDVNGDNCAVTQATAGGRRITIGGRWQADYARSSSGPCFGTAWSVYAGARDC...

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_003511`
TK1151 ID	TkA01G348870
OH-1004 ID	LXL04_003511
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	66.300
Protein coverage (%)	TK1151 74.242 / OH-1004 14.126 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_003511

Location Chr01:81626454-81628780 (-)

Description Similar to RIE1: E3 ubiquitin protein ligase RIE1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g01735`	Probable E3 ubiquitin-protein ligase required for embryo development.	A RING-H2 zinc-finger protein gene RIE1 is essential for seed development in Arabidopsis.2003 · DOI: 10.1023/b:plan.0000009256.01620.a6
`At4g11680`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At1g12760`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At1g63170`	Mediates E2-dependent protein ubiquitination.	No verified direct reference in this release
`At2g01730`	Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition.	Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies.2009 · DOI: 10.1104/pp.109.142729

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003511 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0010197 polar nucleus fusion Biological Process

GO:0016180 snRNA processing Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane Cellular Component

GO:0004521 RNA endonuclease activity Molecular Function

GO:0004842 ubiquitin-protein transferase activity Molecular Function

KEGG gene cross-reference

ath:AT1G12760

ath:AT1G63170

ath:AT2G01730

ath:AT2G01735

ath:AT4G11680

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.

Endoplasmic reticulum0.298

Rank 1 · LXL04_003511 · OH-1004

Nucleus0.238

Rank 2 · LXL04_003511 · OH-1004

Cell membrane0.237

Rank 3 · LXL04_003511 · OH-1004

Cytoplasm0.226

Rank 4 · LXL04_003511 · OH-1004

Golgi apparatus0.171

Rank 5 · LXL04_003511 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13639.13zf-RING_2486-528 aa

PF17123.12zf-RING_11486-514 aa

PF12678.14zf-rbx1486-528 aa

PF13923.13zf-C3HC4_2487-527 aa

PF00097.32zf-C3HC4487-527 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003511	`PF13639.13`	zf-RING_2	486	528	1.5e-14	54.7
LXL04_003511	`PF17123.12`	zf-RING_11	486	514	1.4e-08	34.9
LXL04_003511	`PF12678.14`	zf-rbx1	486	528	2e-08	35.0
LXL04_003511	`PF13923.13`	zf-C3HC4_2	487	527	6.2e-07	29.8
LXL04_003511	`PF00097.32`	zf-C3HC4	487	527	6.9e-06	26.5

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
`Q8GUU2`	Arabidopsis thaliana	E3 ubiquitin protein ligase RIE1	61.694%	Swiss-Prot	weak database homology
`Q93Z92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At4g11680	51.200%	Swiss-Prot	weak database homology
`Q9LN71`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g12760	54.751%	Swiss-Prot	weak database homology
`Q8LDB8`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g63170	48.708%	Swiss-Prot	weak database homology
`Q8GUU3`	Arabidopsis thaliana	Cleavage and polyadenylation specificity factor subunit 3-II	43.537%	Swiss-Prot	weak database homology

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