LXL04_001756 | RubberDandelionOmics

Gene overview

LXL04_001756

Reference: OH-1004 Chr: Chr01 Coordinates: 32576106-32576637 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

444 bp · LXL04_001756|LXL04_001756|OH1004|cDNA

ATGAGGTGCCTCGACTGTGGGAACAAAGCAAAGAAGGATTGTTTATACTACCGGTGTAGGAGTTGTTGCAGAGGACATGGATTTAATTGTCAAACTCATGTTAAGAGCACTTGGGTTCCGGTTTCTACAAGACAAATGGTTGTGCAAAACTCAATAACAACCTCTTATGCTGAacaacaagaagaagaagagttGTATCTTCCATCATCATCTGGCATTGGAGGGCAATTTTCGATGGAGGTGAAAAGCGAAGCTACATT...

CDS

Download CDS FASTA

444 bp · LXL04_001756|LXL04_001756|OH1004|CDS

ATGAGGTGCCTCGACTGTGGGAACAAAGCAAAGAAGGATTGTTTATACTACCGGTGTAGGAGTTGTTGCAGAGGACATGGATTTAATTGTCAAACTCATGTTAAGAGCACTTGGGTTCCGGTTTCTACAAGACAAATGGTTGTGCAAAACTCAATAACAACCTCTTATGCTGAACAACAAGAAGAAGAAGAGTTGTATCTTCCATCATCATCTGGCATTGGAGGGCAATTTTCGATGGAGGTGAAAAGCGAAGCTACATT...

Protein

Download Protein FASTA

147 aa · LXL04_001756|LXL04_001756|OH1004|PROTEIN

MRCLDCGNKAKKDCLYYRCRSCCRGHGFNCQTHVKSTWVPVSTRQMVVQNSITTSYAEQQEEEELYLPSSSGIGGQFSMEVKSEATFTRVRVATTTRENGVMDQYAYETSINIGGHIFKGILYDQGPYPPMVDSREMNVHEEDLFQI

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_001756`
TK1151 ID	TkA01G514880
OH-1004 ID	LXL04_001756
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.100
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_001756

Location Chr01:32576106-32576637 (-)

Description Similar to SRS3: Protein SHI RELATED SEQUENCE 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g21400`	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
`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
`At5g66350`	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.	No verified direct reference in this release
`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
`At4g36260`	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.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001756 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009555 pollen development Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009851 auxin biosynthetic process Biological Process

GO:0009938 negative regulation of gibberellic acid mediated signaling pathway Biological Process

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

GO:0048653 anther development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G75520

ath:AT2G21400

ath:AT3G51060

ath:AT4G36260

ath:AT5G66350

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.

Nucleus0.938

Rank 1 · LXL04_001756 · OH-1004

Cytoplasm0.153

Rank 2 · LXL04_001756 · OH-1004

Cell membrane0.029

Rank 3 · LXL04_001756 · OH-1004

Endoplasmic reticulum0.029

Rank 4 · LXL04_001756 · OH-1004

Plastid0.013

Rank 5 · LXL04_001756 · 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.

PF05142.18DUF7021-62 aa

PF05142.18DUF70263-127 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001756	`PF05142.18`	DUF702	1	62	2.4e-39	136.0
LXL04_001756	`PF05142.18`	DUF702	63	127	2.4e-39	136.0

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
`Q9SJT8`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 3	42.953%	Swiss-Prot	moderate database homology
`Q9LQZ5`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 5	42.593%	Swiss-Prot	moderate database homology
`Q9XGX0`	Arabidopsis thaliana	Protein SHORT INTERNODES	42.069%	Swiss-Prot	moderate database homology
`Q9SD40`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 1	43.750%	Swiss-Prot	moderate database homology
`O65517`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 2	37.821%	Swiss-Prot	moderate database homology

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