LXL04_005996 | RubberDandelionOmics

Gene overview

LXL04_005996

Reference: OH-1004 Chr: Chr01 Coordinates: 176741820-176748945 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1950 bp · LXL04_005996|LXL04_005996|OH1004|cDNA

ATGGAGAAGGCAGGCGCCGACATGGAGGATGGCGATGGATGCAAGCAGCAGAGAAAAACGGAGGTTGAAGCAGCATCGACTGAAGTTTGGTTGTCGATTGTGGTGTTGGTGACCGATGTAGTTGGCAACCATATTTGTGGTTTTCGGTTGATATTCACCGTTCTACTTCCACAATCACGTCGCGCAACCGCGAGAAAAGATGGTCCTGGCGGAACAGGAAAAACATATTTGTACAAAGCATTACTAGCTAATGTTCGCAA...

CDS

Download CDS FASTA

1950 bp · LXL04_005996|LXL04_005996|OH1004|CDS

ATGGAGAAGGCAGGCGCCGACATGGAGGATGGCGATGGATGCAAGCAGCAGAGAAAAACGGAGGTTGAAGCAGCATCGACTGAAGTTTGGTTGTCGATTGTGGTGTTGGTGACCGATGTAGTTGGCAACCATATTTGTGGTTTTCGGTTGATATTCACCGTTCTACTTCCACAATCACGTCGCGCAACCGCGAGAAAAGATGGTCCTGGCGGAACAGGAAAAACATATTTGTACAAAGCATTACTAGCTAATGTTCGCAA...

Protein

Download Protein FASTA

649 aa · LXL04_005996|LXL04_005996|OH1004|PROTEIN

MEKAGADMEDGDGCKQQRKTEVEAASTEVWLSIVVLVTDVVGNHICGFRLIFTVLLPQSRRATARKDGPGGTGKTYLYKALLANVRKCGHIALATASSGVAANNMPGGRTAHSRFKIPLNLENNSACNVKKQSGTAQLLRIAKLIIWDEASMAKRQAVEAFDRTMQDIIGVTLPFGGKIMVMGGDFRQVLPVTDPWFSDFLLRVGDGVEGTEDGSLIRIPDDRVIPYNDNSISLDALIDAIFPTLDVNMSRSDYIISRAI...

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_005996`
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_005996

Location Chr01:176741820-176748945 (+)

Description Similar to UEV1D: Ubiquitin-conjugating enzyme E2 variant 1D

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g52560`	Has no ubiquitin ligase activity on its own.	Arabidopsis UEV1D promotes Lysine-63-linked polyubiquitination and is involved in DNA damage response.2008 · DOI: 10.1105/tpc.107.051862
`At2g36060`	Has no ubiquitin ligase activity on its own.	No verified direct reference in this release
`At1g70660`	Has no ubiquitin ligase activity on its own.	No verified direct reference in this release
`At1g23260`	Has no ubiquitin ligase activity on its own.	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_005996 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000723 telomere maintenance Biological Process

GO:0006281 DNA repair Biological Process

GO:0006301 DNA damage tolerance Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006974 DNA damage response Biological Process

GO:0070534 protein K63-linked ubiquitination Biological Process

GO:1902916 positive regulation of protein polyubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT1G23260

ath:AT1G70660

ath:AT2G36060

ath:AT3G52560

xla:734585

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.

Nucleus0.532

Rank 1 · LXL04_005996 · OH-1004

Cytoplasm0.428

Rank 2 · LXL04_005996 · OH-1004

Mitochondrion0.065

Rank 3 · LXL04_005996 · OH-1004

Cell membrane0.042

Rank 4 · LXL04_005996 · OH-1004

Endoplasmic reticulum0.036

Rank 5 · LXL04_005996 · 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.

PF05970.21PIF167-193 aa

PF21530.4Pif1_2B_dom303-346 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005996	`PF05970.21`	PIF1	67	193	2.3e-49	168.7
LXL04_005996	`PF21530.4`	Pif1_2B_dom	303	346	5.5e-20	71.5

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9SVD7`	Arabidopsis thaliana	Ubiquitin-conjugating enzyme E2 variant 1D	70.909%	Swiss-Prot	weak database homology
`Q9SJ44`	Arabidopsis thaliana	Ubiquitin-conjugating enzyme E2 variant 1C	70.909%	Swiss-Prot	weak database homology
`Q9CAB6`	Arabidopsis thaliana	Ubiquitin-conjugating enzyme E2 variant 1B	62.500%	Swiss-Prot	weak database homology
`Q93YP0`	Arabidopsis thaliana	Ubiquitin-conjugating enzyme E2 variant 1A	54.545%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card