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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_002884
Reference: OH-1004 Chr: Chr01 Coordinates: 60263604-60266676 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1455 bp · LXL04_002884|LXL04_002884|OH1004|cDNA

ATGAGGTTCTTCAACCTTATGGGGAACTCCTTTGGGTGCTCGGCATCTGGAGAACGCCTTGTTTCGGCTGCAAGAGATGGCGATGTTCAAGAAGCCAAAGCCTTGCTCGAATATAACCCTCGACTTGCTAAATACTCAACTTTTGGTGTTCGGAATTCCCCCCTTCATTACTCTGCTGCCCAAGGTCACCATGAGATTGTTTCGCTCTTGATTGAATCTGGCGTTGATATCAACCTCAGGAATTATCGTGGCCAGACTGC...

CDS

Download CDS FASTA

1455 bp · LXL04_002884|LXL04_002884|OH1004|CDS

ATGAGGTTCTTCAACCTTATGGGGAACTCCTTTGGGTGCTCGGCATCTGGAGAACGCCTTGTTTCGGCTGCAAGAGATGGCGATGTTCAAGAAGCCAAAGCCTTGCTCGAATATAACCCTCGACTTGCTAAATACTCAACTTTTGGTGTTCGGAATTCCCCCCTTCATTACTCTGCTGCCCAAGGTCACCATGAGATTGTTTCGCTCTTGATTGAATCTGGCGTTGATATCAACCTCAGGAATTATCGTGGCCAGACTGC...

Protein

Download Protein FASTA

484 aa · LXL04_002884|LXL04_002884|OH1004|PROTEIN

MRFFNLMGNSFGCSASGERLVSAARDGDVQEAKALLEYNPRLAKYSTFGVRNSPLHYSAAQGHHEIVSLLIESGVDINLRNYRGQTALMQACQYGHWEVVLTLVLYKANIHKADYLNGGTALHLAALNGQSRCIRILHADYIPSVPNFLELVNGKSRIEEFVCESNEGSLYKTINRAADGGVTALHMAALNGHFDSVHLLIDLGASVTEVTVEDGTTIDLIGAGSTPLHYAACGGNAQCCQILIAKGASLTAQNAKGWTP...

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_002884
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_002884
LocationChr01:60263604-60266676 (-)
DescriptionSimilar to XBOS32: Probable E3 ubiquitin-protein ligase XBOS32
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g57740 E3 ubiquitin-protein ligase that mediates ubiquitination of ACC synthases (ACS).
The ubiquitin ligase XBAT32 regulates lateral root development in Arabidopsis.2004 · DOI: 10.1111/j.1365-313x.2004.02266.x
Arabidopsis RING E3 ligase XBAT32 regulates lateral root production through its role in ethylene biosynthesis.2010 · DOI: 10.1104/pp.110.156976
At5g07270 Possesses E3 ubiquitin-protein ligase activity when associated with the E2 enzyme UBC8 in vitro. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
Os02g0791200 Probable E3 ubiquitin-protein ligase XBOS32. No verified direct reference in this release
Os08g0258200 Probable E3 ubiquitin-protein ligase XBOS35. No verified direct reference in this release
Os10g0521600 Probable E3 ubiquitin-protein ligase XBOS33. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_002884 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006511 ubiquitin-dependent protein catabolic process Biological Process
GO:0009733 response to auxin Biological Process
GO:0010311 lateral root formation Biological Process
GO:0010366 negative regulation of ethylene biosynthetic process Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0051865 protein autoubiquitination Biological Process
GO:0005737 cytoplasm 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:AT5G07270
ath:AT5G57740
dosa:Os02g0791200
dosa:Os08g0258200
dosa:Os10g0521600
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.

Cytoplasm0.542
Rank 1 · LXL04_002884 · OH-1004
Nucleus0.316
Rank 2 · LXL04_002884 · OH-1004
Cell membrane0.169
Rank 3 · LXL04_002884 · OH-1004
Golgi apparatus0.097
Rank 4 · LXL04_002884 · OH-1004
Mitochondrion0.088
Rank 5 · LXL04_002884 · 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.

PF12796.14Ank_221-113 aa
PF00023.37Ank52-81 aa
PF13606.13Ank_352-78 aa
PF13637.13Ank_455-103 aa
PF13857.13Ank_570-108 aa
PF12796.14Ank_284-138 aa
PF00023.37Ank84-114 aa
PF13606.13Ank_384-111 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_002884PF12796.14Ank_2211131.4e-39135.2
LXL04_002884PF00023.37Ank52815.9e-36121.2
LXL04_002884PF13606.13Ank_352784e-2791.7
LXL04_002884PF13637.13Ank_4551033e-2898.0
LXL04_002884PF13857.13Ank_5701082e-2795.7
LXL04_002884PF12796.14Ank_2841381.4e-39135.2
LXL04_002884PF00023.37Ank841145.9e-36121.2
LXL04_002884PF13606.13Ank_3841114e-2791.7
LXL04_002884PF13637.13Ank_4881383e-2898.0
LXL04_002884PF12796.14Ank_21092081.4e-39135.2
LXL04_002884PF13637.13Ank_41742013e-2898.0
LXL04_002884PF13857.13Ank_51752202e-2795.7
LXL04_002884PF00023.37Ank1812095.9e-36121.2
LXL04_002884PF13606.13Ank_31812074e-2791.7
LXL04_002884PF13637.13Ank_41852443e-2898.0
LXL04_002884PF12796.14Ank_22232701.4e-39135.2

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q6NLQ8Arabidopsis thalianaE3 ubiquitin-protein ligase XBAT3261.702%Swiss-Protstrong database homology
Q4FE45Arabidopsis thalianaE3 ubiquitin-protein ligase XBAT3351.634%Swiss-Protstrong database homology
Q6KAE5Oryza sativa subsp. japonicaProbable E3 ubiquitin-protein ligase XBOS3261.179%Swiss-Protstrong database homology
Q7EZ44Oryza sativa subsp. japonicaProbable E3 ubiquitin-protein ligase XBOS3562.245%Swiss-Protstrong database homology
Q337A0Oryza sativa subsp. japonicaProbable E3 ubiquitin-protein ligase XBOS3352.155%Swiss-Protstrong database homology

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