LXL04_024403 | RubberDandelionOmics

Gene overview

LXL04_024403

Reference: OH-1004 Chr: Chr05 Coordinates: 89683105-89686295 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1860 bp · LXL04_024403|LXL04_024403|OH1004|cDNA

ATGGATACTTTGTTTAGGCTTGTCAGCCTCCAAAAACAACCCTCTCGCCATCATCatctccaccaccaccaccaacaCCATCATTCCACCAACTCCACCAGTAGAACTTCAAGCAGTTCCAGATCATCCACCCAAACTCCATCTCCCTTCAATTACCAACAAGGAGAAGATCAAGAAGAATGCTTCAACTTTTTCATGGATGACGAAGATTTCTCATCTTCTTCCTCAAGGAACCCCCACCAAAATCAGTACTACTCTTC...

CDS

Download CDS FASTA

1860 bp · LXL04_024403|LXL04_024403|OH1004|CDS

ATGGATACTTTGTTTAGGCTTGTCAGCCTCCAAAAACAACCCTCTCGCCATCATCATCTCCACCACCACCACCAACACCATCATTCCACCAACTCCACCAGTAGAACTTCAAGCAGTTCCAGATCATCCACCCAAACTCCATCTCCCTTCAATTACCAACAAGGAGAAGATCAAGAAGAATGCTTCAACTTTTTCATGGATGACGAAGATTTCTCATCTTCTTCCTCAAGGAACCCCCACCAAAATCAGTACTACTCTTC...

Protein

Download Protein FASTA

619 aa · LXL04_024403|LXL04_024403|OH1004|PROTEIN

MDTLFRLVSLQKQPSRHHHLHHHHQHHHSTNSTSRTSSSSRSSTQTPSPFNYQQGEDQEECFNFFMDDEDFSSSSSRNPHQNQYYSSQQPHFHHQSSSTPTPTTSTTTTPPPFSHYGFSSSEHQQSSDPNINYSYSPARDVTMEFSNSFSGNTWASDVLLDAARAVADKNSGRLQQLMWMLNELSSPYGDTDQKLSSYFLQALFSRMTDSGDRSYRTLTSASDKMCSFESTRKLVLKFQEVSPWTTFGHVACNGAIMEAF...

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_024403`
TK1151 ID	TkA06G147170
OH-1004 ID	LXL04_024403
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	87.000
Protein coverage (%)	TK1151 98.753 / OH-1004 85.945 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_024403

Location Chr05:89683105-89686295 (-)

Description Similar to SHR: Protein SHORT-ROOT

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g37650`	Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots.	Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana.1998 · DOI: 10.1046/j.1365-313x.1998.00137.x

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2YN56`	Transcription factor required for the asymmetric cell division involved in radial pattern formation in roots.	No verified direct reference in this release
`Os07g0586900`	Transcription factor required for the asymmetric cell division involved in radial pattern formation in roots.	No verified direct reference in this release
`Os03g0433200`	Putative transcription factor involved in asymmetric cell division.	No verified direct reference in this release
`UniProt: A2XIA8`	Putative transcription factor involved in asymmetric cell division.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024403 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0008356 asymmetric cell division Biological Process

GO:0009956 radial pattern formation Biological Process

GO:0032350 regulation of hormone metabolic process Biological Process

GO:0045930 negative regulation of mitotic cell cycle Biological Process

GO:0048366 leaf development Biological Process

GO:0060586 multicellular organismal-level iron ion homeostasis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005769 early endosome Cellular Component

GO:0005770 late endosome Cellular Component

GO:0055037 recycling endosome Cellular Component

KEGG gene cross-reference

ath:AT4G37650

dosa:Os03g0433200

dosa:Os07g0586900

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.739

Rank 1 · LXL04_024403 · OH-1004

Cytoplasm0.263

Rank 2 · LXL04_024403 · OH-1004

Cell membrane0.095

Rank 3 · LXL04_024403 · OH-1004

Endoplasmic reticulum0.045

Rank 4 · LXL04_024403 · OH-1004

Plastid0.030

Rank 5 · LXL04_024403 · 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.

PF03514.21GRAS157-532 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024403	`PF03514.21`	GRAS	157	532	1.1e-94	318.1

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

Protein	Organism	Description	Identity	Database	Confidence
`Q9SZF7`	Arabidopsis thaliana	Protein SHORT-ROOT	57.195%	Swiss-Prot	strong database homology
`A2YN56`	Oryza sativa subsp. indica	Protein SHORT-ROOT 1	45.757%	Swiss-Prot	moderate database homology
`Q8H2X8`	Oryza sativa subsp. japonica	Protein SHORT-ROOT 1	45.757%	Swiss-Prot	moderate database homology
`Q75I13`	Oryza sativa subsp. japonica	Protein SHORT-ROOT 2	48.757%	Swiss-Prot	moderate database homology
`A2XIA8`	Oryza sativa subsp. indica	Protein SHORT-ROOT 2	53.810%	Swiss-Prot	moderate database homology

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