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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_035544
Reference: OH-1004 Chr: Chr08 Coordinates: 24355976-24358300 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1068 bp · LXL04_035544|LXL04_035544|OH1004|cDNA

ATGTCACAAGAAGTCTACAGCGTCGGCGGTGGTAACGGTGGCGACGGTGCGGCCCCTCAAATATACTTCTGTTACCAATGCAATCGTACGGTGTCCATCAGACCTGCGCCGACCGCCTCCTCCGAACTCTTTTGTCCCAATTGTAACGGTGGGTTCCTAGAGGAATACgaaaaccctaaccctagccTGGGAACCCCAAATCCCTTTCTCCCATTCGAAGATGCTCCGCCTTTCCCCTCATTCTCTTCTGGCTTTCCGTT...

CDS

Download CDS FASTA

1068 bp · LXL04_035544|LXL04_035544|OH1004|CDS

ATGTCACAAGAAGTCTACAGCGTCGGCGGTGGTAACGGTGGCGACGGTGCGGCCCCTCAAATATACTTCTGTTACCAATGCAATCGTACGGTGTCCATCAGACCTGCGCCGACCGCCTCCTCCGAACTCTTTTGTCCCAATTGTAACGGTGGGTTCCTAGAGGAATACGAAAACCCTAACCCTAGCCTGGGAACCCCAAATCCCTTTCTCCCATTCGAAGATGCTCCGCCTTTCCCCTCATTCTCTTCTGGCTTTCCGTT...

Protein

Download Protein FASTA

355 aa · LXL04_035544|LXL04_035544|OH1004|PROTEIN

MSQEVYSVGGGNGGDGAAPQIYFCYQCNRTVSIRPAPTASSELFCPNCNGGFLEEYENPNPSLGTPNPFLPFEDAPPFPSFSSGFPLVFSSTPRAGAGSGDFQNPNDLSALFGGPMSRPGGVQNPGEFNPFAFLQNYLNTLRAGGANIQFVIENNTDGDPSGFRLPSNLGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAVENLPNIKITKQLLESDYSDCAVCKDSFELEEEAKQLPCKHMYHPDCIMPWLELHNSC...

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_035544
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_035544
LocationChr08:24355976-24358300 (+)
DescriptionSimilar to RING1: E3 ubiquitin-protein ligase RING1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g19950 E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. No verified direct reference in this release
At3g56580 E3 ubiquitin-protein ligase that promotes osmotic stress and abscisic acid (ABA) responses.
The atrzf1 mutation of the novel RING-type E3 ubiquitin ligase increases proline contents and enhances drought tolerance in Arabidopsis.2013 · DOI: 10.1016/j.plantsci.2012.12.007
PCA22 acts as a suppressor of atrzf1 to mediate proline accumulation in response to abiotic stress in Arabidopsis.2017 · DOI: 10.1093/jxb/erx069
At2g40830 Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
Os05g0488800 Possesses E3 ubiqutin-protein ligase activity in vitro.
Molecular dissection of Oryza sativa salt-induced RING Finger Protein 1 (OsSIRP1): possible involvement in the sensitivity response to salinity stress.2016 · DOI: 10.1111/ppl.12459
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_035544 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006511 ubiquitin-dependent protein catabolic process Biological Process
GO:0006970 response to osmotic stress Biological Process
GO:0009414 response to water deprivation Biological Process
GO:0009651 response to salt stress Biological Process
GO:0009738 abscisic acid-activated signaling pathway Biological Process
GO:0009938 negative regulation of gibberellic acid mediated signaling pathway Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0047484 regulation of response to osmotic stress Biological Process
GO:0090378 seed trichome elongation Biological Process
GO:1902006 negative regulation of L-proline biosynthetic process Biological Process
GO:0005634 nucleus Cellular Component
GO:0005737 cytoplasm Cellular Component
KEGG gene cross-reference
ath:AT2G40830
ath:AT3G19950
ath:AT3G56580
dosa:Os05g0488800
osa:4339152
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.

Cytoplasm0.656
Rank 1 · LXL04_035544 · OH-1004
Nucleus0.383
Rank 2 · LXL04_035544 · OH-1004
Endoplasmic reticulum0.104
Rank 3 · LXL04_035544 · OH-1004
Golgi apparatus0.068
Rank 4 · LXL04_035544 · OH-1004
Lysosome / Vacuole0.062
Rank 5 · LXL04_035544 · 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.

PF14369.12Zn_ribbon_1921-56 aa
PF13639.13zf-RING_2222-264 aa
PF17123.12zf-RING_11222-250 aa
PF13923.13zf-C3HC4_2223-263 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_035544PF14369.12Zn_ribbon_1921561.4e-1351.4
LXL04_035544PF13639.13zf-RING_22222641.2e-1248.6
LXL04_035544PF17123.12zf-RING_112222507.2e-0832.7
LXL04_035544PF13923.13zf-C3HC4_22232631.2e-0835.3

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
Q8LPN7Arabidopsis thalianaE3 ubiquitin-protein ligase RING1-like53.608%Swiss-Protstrong database homology
Q94AK4Arabidopsis thalianaE3 ubiquitin-protein ligase RZF137.652%Swiss-Protmoderate database homology
O22197Arabidopsis thalianaProbable E3 ubiquitin-protein ligase RHC1A36.122%Swiss-Protmoderate database homology
Q6AVN2Oryza sativa subsp. japonicaE3 ubiquitin-protein ligase SIRP133.708%Swiss-Protmoderate database homology

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