LXL04_021897 | RubberDandelionOmics

Gene overview

LXL04_021897

Reference: OH-1004 Chr: Chr04 Coordinates: 139785105-139789632 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1617 bp · LXL04_021897|LXL04_021897|OH1004|cDNA

ATGATGCCATTGTTCTCCTCCCCACCTCTCTCTGGTCTCTATCTCCATCTCACTCCTTTTTTTCAGTTTCACAATTTGTCTTTTCGCATTCTTGAATTCCCGGTGGCCAAACCAAAGCCAATCTACACCACTCATGCCTTCTTCAGGGAACGTCACCCACCTCTCTCAGCCTTGTATCTACGGAAGTCGGGGTTCATGAAATGGCTGAGCAAGCTTCTTAAAGGTGGATCAAATCGTGGATCGGTCAGTACTGGAAATCC...

CDS

Download CDS FASTA

1617 bp · LXL04_021897|LXL04_021897|OH1004|CDS

ATGATGCCATTGTTCTCCTCCCCACCTCTCTCTGGTCTCTATCTCCATCTCACTCCTTTTTTTCAGTTTCACAATTTGTCTTTTCGCATTCTTGAATTCCCGGTGGCCAAACCAAAGCCAATCTACACCACTCATGCCTTCTTCAGGGAACGTCACCCACCTCTCTCAGCCTTGTATCTACGGAAGTCGGGGTTCATGAAATGGCTGAGCAAGCTTCTTAAAGGTGGATCAAATCGTGGATCGGTCAGTACTGGAAATCC...

Protein

Download Protein FASTA

538 aa · LXL04_021897|LXL04_021897|OH1004|PROTEIN

MMPLFSSPPLSGLYLHLTPFFQFHNLSFRILEFPVAKPKPIYTTHAFFRERHPPLSALYLRKSGFMKWLSKLLKGGSNRGSVSTGNPPQFIGDESMVLRAPVRSLDTRSRSDKEKEELDRAIALSLAEGLKKPNGYGWQPGNDNDIEKPHQDDFHPSYPPYVGYRICGGCNRDIGYNNYLGCMGTFFHPDCFCCRACNYPITEHEFSLSGKDAYHKSCFKELTHPKCEVCFQFIPANGAGLIEYRCHPFWSQKYCPAHEH...

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_021897`
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_021897

Location Chr04:139785105-139789632 (-)

Description Similar to DAR2: Protein DA1-related 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g39830`	Acts redundantly with DA1 and DAR1 to regulate endoreduplication during leaf development.	Arabidopsis Lateral Root Development 3 is essential for early phloem development and function, and hence for normal root system development.2011 · DOI: 10.1111/j.1365-313x.2011.04700.x Control of root meristem size by DA1-RELATED PROTEIN2 in Arabidopsis.2013 · DOI: 10.1104/pp.112.210237 The ubiquitin receptors DA1, DAR1, and DAR2 redundantly regulate endoreduplication by modulating the stability of TCP14/15 in Arabidopsis.2015 · DOI: 10.1105/tpc.114.132274
`At4g36860`	Acts redundantly with DA1 and DAR2 to regulate endoreduplication during leaf development.	The ubiquitin receptors DA1, DAR1, and DAR2 redundantly regulate endoreduplication by modulating the stability of TCP14/15 in Arabidopsis.2015 · DOI: 10.1105/tpc.114.132274
`At1g19270`	Ubiquitin receptor that limits final seed and organ size by restricting the period of cell proliferation.	No verified direct reference in this release
`At5g66620`	Ubiquitin receptor that probably regulates developmental process.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0267800`	Ubiquitin receptor that functions as a positive regulator of grain size and weight.	The ubiquitin-interacting motif-type ubiquitin receptor HDR3 interacts with and stabilizes the histone acetyltransferase GW6a to control the grain size in rice.2021 · DOI: 10.1093/plcell/koab194

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021897 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0009825 multidimensional cell growth Biological Process

GO:0010088 phloem development Biological Process

GO:0032875 regulation of DNA endoreduplication Biological Process

GO:0046620 regulation of organ growth Biological Process

GO:0046621 negative regulation of organ growth Biological Process

GO:0048317 seed morphogenesis Biological Process

GO:0048364 root development Biological Process

GO:0048482 plant ovule morphogenesis Biological Process

GO:0080113 regulation of seed growth Biological Process

GO:1900057 positive regulation of leaf senescence Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G19270

ath:AT2G39830

ath:AT4G36860

ath:AT5G66620

dosa:Os03g0267800

osa:4332368

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.

Nucleus0.452

Rank 1 · LXL04_021897 · OH-1004

Cytoplasm0.364

Rank 2 · LXL04_021897 · OH-1004

Cell membrane0.176

Rank 3 · LXL04_021897 · OH-1004

Endoplasmic reticulum0.068

Rank 4 · LXL04_021897 · OH-1004

Lysosome / Vacuole0.058

Rank 5 · LXL04_021897 · 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.

PF00412.29LIM167-221 aa

PF12315.15DA1-like322-531 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021897	`PF00412.29`	LIM	167	221	3.3e-07	31.2
LXL04_021897	`PF12315.15`	DA1-like	322	531	1.5e-87	293.2

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

Protein	Organism	Description	Identity	Database	Confidence
`Q0WSN2`	Arabidopsis thaliana	Protein DA1-related 2	68.200%	Swiss-Prot	strong database homology
`Q8W4F0`	Arabidopsis thaliana	Protein DA1-related 1	55.604%	Swiss-Prot	strong database homology
`P0C7Q8`	Arabidopsis thaliana	Protein DA1	45.126%	Swiss-Prot	moderate database homology
`Q9FJX8`	Arabidopsis thaliana	Protein DA1-related 6	41.558%	Swiss-Prot	moderate database homology
`Q10NJ6`	Oryza sativa subsp. japonica	LIM domain-containing protein HDR3	56.746%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card