LXL04_003103 | RubberDandelionOmics

Gene overview

LXL04_003103

Reference: OH-1004 Chr: Chr01 Coordinates: 67610214-67610893 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

606 bp · LXL04_003103|LXL04_003103|OH1004|cDNA

ATGATCATGATGCAGTATTATCAGCTtcaccaacaccaacaccaacacaAGCACCGACAACAGCTCCTCCACCAGCAATCGCATTATGAATTCGCCGTCAGTAGTCGTACCGATCAGAAGAGAAGTAGTAGCGTCAGTAGCGGAGGCGGAGGCGGAGGTGGTGGCGTGGATGATCTTAATCGCAGCAACGTTGATCAGTTGGCGTCTTCCTGGAACATATTCGGTGGAGGAAGATCGGTCGagggtggtggtggcggtga...

CDS

Download CDS FASTA

606 bp · LXL04_003103|LXL04_003103|OH1004|CDS

ATGATCATGATGCAGTATTATCAGCTTCACCAACACCAACACCAACACAAGCACCGACAACAGCTCCTCCACCAGCAATCGCATTATGAATTCGCCGTCAGTAGTCGTACCGATCAGAAGAGAAGTAGTAGCGTCAGTAGCGGAGGCGGAGGCGGAGGTGGTGGCGTGGATGATCTTAATCGCAGCAACGTTGATCAGTTGGCGTCTTCCTGGAACATATTCGGTGGAGGAAGATCGGTCGAGGGTGGTGGTGGCGGTGA...

Protein

Download Protein FASTA

201 aa · LXL04_003103|LXL04_003103|OH1004|PROTEIN

MIMMQYYQLHQHQHQHKHRQQLLHQQSHYEFAVSSRTDQKRSSSVSSGGGGGGGGVDDLNRSNVDQLASSWNIFGGGRSVEGGGGGDSKEMRQGGYGIGGGSGSGSGGGGGVNCQDCGNQAKKDCQHMRCRTCCKARGYHCQTHVKSTWVPAGKRREHQQQLVSLTQQQSLGNQKKLSLMMRATRVVNPSSTYLVFSIFFF

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_003103`
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_003103

Location Chr01:67610214-67610893 (+)

Description Similar to SRS5: Protein SHI RELATED SEQUENCE 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g75520`	Transcription activator that binds DNA on 5'-ACTCTAC-3' and promotes auxin homeostasis-regulating gene expression (e.g. YUC genes), as well as genes affecting stamen development, cell expansion and timing of flowering.	Functionally redundant SHI family genes regulate Arabidopsis gynoecium development in a dose-dependent manner.2006 · DOI: 10.1111/j.1365-313x.2006.02774.x
`At3g51060`	Transcription activator that binds DNA on 5'-ACTCTAC-3' and promotes auxin homeostasis-regulating gene expression (e.g. YUC genes), as well as genes affecting stamen development, cell expansion and timing of flowering.	STY1 and STY2 promote the formation of apical tissues during Arabidopsis gynoecium development.2002 · DOI: 10.1242/dev.129.20.4707 STY1 regulates auxin homeostasis and affects apical-basal patterning of the Arabidopsis gynoecium.2006 · DOI: 10.1111/j.1365-313x.2006.02775.x Functionally redundant SHI family genes regulate Arabidopsis gynoecium development in a dose-dependent manner.2006 · DOI: 10.1111/j.1365-313x.2006.02774.x Auxin can act independently of CRC, LUG, SEU, SPT and STY1 in style development but not apical-basal patterning of the Arabidopsis gynoecium.2008 · DOI: 10.1111/j.1469-8137.2008.02625.x The Arabidopsis thaliana STYLISH1 protein acts as a transcriptional activator regulating auxin biosynthesis.2010 · DOI: 10.1105/tpc.108.064816 The Arabidopsis thaliana transcriptional activator STYLISH1 regulates genes affecting stamen development, cell expansion and timing of flowering.2012 · DOI: 10.1007/s11103-012-9888-z
`At1g19790`	Transcription activator that binds DNA on 5'-ACTCTAC-3' and promotes auxin homeostasis-regulating gene expression (e.g. YUC genes), as well as genes affecting stamen development, cell expansion and timing of flowering.	Functionally redundant SHI family genes regulate Arabidopsis gynoecium development in a dose-dependent manner.2006 · DOI: 10.1111/j.1365-313x.2006.02774.x Activation tagging of an Arabidopsis SHI-RELATED SEQUENCE gene produces abnormal anther dehiscence and floral development.2010 · DOI: 10.1007/s11103-010-9677-5

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0531600`	Regulates tillering and panicle branching by modulating SPL14/IPA1 transcriptional activity on the downstream TB1 and DEP1 target genes.	OsSHI1 Regulates Plant Architecture Through Modulating the Transcriptional Activity of IPA1 in Rice.2019 · DOI: 10.1105/tpc.19.00023

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003103 · 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:0009299 mRNA transcription Biological Process

GO:0009555 pollen development Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009851 auxin biosynthetic process Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0048450 floral organ structural organization Biological Process

GO:0048653 anther development Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G19790

ath:AT1G75520

ath:AT3G51060

dosa:Os09g0531600

osa:4347669

sly:101251254

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.

Nucleus0.984

Rank 1 · LXL04_003103 · OH-1004

Cytoplasm0.072

Rank 2 · LXL04_003103 · OH-1004

Cell membrane0.018

Rank 3 · LXL04_003103 · OH-1004

Endoplasmic reticulum0.012

Rank 4 · LXL04_003103 · OH-1004

Plastid0.007

Rank 5 · LXL04_003103 · 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.

PF05142.18DUF702111-176 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003103	`PF05142.18`	DUF702	111	176	1.8e-31	110.4

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
`Q9LQZ5`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 5	83.929%	Swiss-Prot	weak database homology
`Q9SD40`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 1	73.333%	Swiss-Prot	weak database homology
`Q9FXH7`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 7	73.333%	Swiss-Prot	weak database homology
`Q652K4`	Oryza sativa subsp. japonica	Protein SHORT INTERNODES 1	82.353%	Swiss-Prot	weak database homology

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