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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_004430
Reference: OH-1004 Chr: Chr01 Coordinates: 135774706-135775869 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

760 bp · LXL04_004430|LXL04_004430|OH1004|cDNA

ATGAACTGGCACCTACAAACTGAATTCAACATCCCCCATAGCTTTATGGATTTCTTTGAAGGACTCACATATGAGCATGTCAATTTCATTTTTTCCGACGTCACATATCCTCAGGATAGCACAAACTATACAATGAATACGAGTTCATATAAGTTTGCATACTCTGAACAGGGGAATTTCTCATACTACGATTATTTTAATGCGTATGCCATAAATGATCCGATATATGGCAACAGTGGATTTACTAGACAACTAGAAAA...

CDS

Download CDS FASTA

756 bp · LXL04_004430|LXL04_004430|OH1004|CDS

ATGAACTGGCACCTACAAACTGAATTCAACATCCCCCATAGCTTTATGGATTTCTTTGAAGGACTCACATATGAGCATGTCAATTTCATTTTTTCCGACGTCACATATCCTCAGGATAGCACAAACTATACAATGAATACGAGTTCATATAAGTTTGCATACTCTGAACAGGGGAATTTCTCATACTACGATTATTTTAATGCGTATGCCATAAATGATCCGATATATGGCAACAGTGGATTTACTAGACAACTAGAAAA...

Protein

Download Protein FASTA

251 aa · LXL04_004430|LXL04_004430|OH1004|PROTEIN

MNWHLQTEFNIPHSFMDFFEGLTYEHVNFIFSDVTYPQDSTNYTMNTSSYKFAYSEQGNFSYYDYFNAYAINDPIYGNSGFTRQLENTPTIANERSTPLHIQQDGHSTSNSHTNPSNCPQSNHNHNPNQNPGDYHQVMWEDNVDLDNMSYEELLELGEVVGSQSRGLSHEAISLLPVSKFKCGFFWRKKSKSERCVICQMEYKRGERQVTLPCKHIYHAGCGSQWLSINKACPICYKEVLINIPKHSEKTK

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.

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ID Mapping

Input IDLXL04_004430
Source versionOH-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 IDLXL04_004430
LocationChr01:135774706-135775869 (+)
DescriptionSimilar to BB: E3 ubiquitin-protein ligase BIG BROTHER
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g63530 E3 ubiquitin-protein ligase that limits organ size, and possibly seed size, in a dose-dependent manner.
Forever Young: The Role of Ubiquitin Receptor DA1 and E3 Ligase BIG BROTHER in Controlling Leaf Growth and Development.2017 · DOI: 10.1104/pp.16.01410
At3g19910 E3 ubiquitin-ligase probably involved in organ size regulation. No verified direct reference in this release
At2g15530 E3 ubiquitin-protein ligase that functions as a regulator of MED25 stability by targeting MED25 for degradation in a RING-H2- dependent way.
Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription.2012 · DOI: 10.1104/pp.112.205500
At4g34040 E3 ubiquitin-protein ligase that functions as a regulator of MED25 stability by targeting MED25 for degradation in a RING-H2- dependent way.
Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription.2012 · DOI: 10.1104/pp.112.205500

Rice

Reference gene IDPossible functionPapers / DOI
Os04g0648800 Probable E3 ubiquitin-protein ligase that functions downstream of HAL3 and is required for HAL3-regulated plant growth. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_004430 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0008285 negative regulation of cell population proliferation Biological Process
GO:0009845 seed germination Biological Process
GO:0009908 flower development Biological Process
GO:0010218 response to far red light Biological Process
GO:0010228 vegetative to reproductive phase transition of meristem Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process
GO:0046621 negative regulation of organ growth Biological Process
GO:0048437 floral organ development Biological Process
GO:0051865 protein autoubiquitination Biological Process
GO:1900057 positive regulation of leaf senescence Biological Process
GO:0005634 nucleus Cellular Component
KEGG gene cross-reference
ath:AT2G15530
ath:AT3G19910
ath:AT3G63530
ath:AT4G34040
dosa:Os04g0648800
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.

Cytoplasm0.513
Rank 1 · LXL04_004430 · OH-1004
Nucleus0.475
Rank 2 · LXL04_004430 · OH-1004
Cell membrane0.087
Rank 3 · LXL04_004430 · OH-1004
Endoplasmic reticulum0.074
Rank 4 · LXL04_004430 · OH-1004
Lysosome / Vacuole0.068
Rank 5 · LXL04_004430 · 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.

PF12678.14zf-rbx1191-235 aa
PF13639.13zf-RING_2194-235 aa
PF13923.13zf-C3HC4_2194-235 aa
PF17123.12zf-RING_11195-221 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_004430PF12678.14zf-rbx11912355.4e-0730.5
LXL04_004430PF13639.13zf-RING_21942353.9e-1350.1
LXL04_004430PF13923.13zf-C3HC4_21942352.1e-0731.3
LXL04_004430PF17123.12zf-RING_111952219.7e-0729.1

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q8L649Arabidopsis thalianaE3 ubiquitin-protein ligase BIG BROTHER40.664%Swiss-Protmoderate database homology
Q9LT17Arabidopsis thalianaE3 ubiquitin ligase BIG BROTHER-related48.077%Swiss-Protweak database homology
Q9ZQF9Arabidopsis thalianaE3 ubiquitin-protein ligase MBR141.525%Swiss-Protweak database homology
O49500Arabidopsis thalianaE3 ubiquitin-protein ligase MBR240.741%Swiss-Protweak database homology
Q7XTV7Oryza sativa subsp. japonicaProbable E3 ubiquitin-protein ligase HIP144.144%Swiss-Protweak database homology

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