LXL04_023314 | RubberDandelionOmics

Gene overview

LXL04_023314

Reference: OH-1004 Chr: Chr05 Coordinates: 32100033-32101503 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1236 bp · LXL04_023314|LXL04_023314|OH1004|cDNA

TTATTTCGTTTGTAGCAGTGGCAGTATCTTCTGATCTTACTGCAAATCTCTGCGGTCATCCCCTACTCTGTGGCTTCCAGCAGGAATACCAGGCTGCCTTCTGATTCTGGTGCGTTTGCGGACTGGGTGGCTAATCCTTCGTCTTCCTCTGCTCTCAGAAATTCTGATCAGGACCTGTCGTTGGGCTTCAATGCCAGTGCCGCCGCCGCTGCGGTTGTTCACGGTGGAGGGTCGACCGGGATTTGGTCCACACCCTCTGC...

CDS

Download CDS FASTA

1206 bp · LXL04_023314|LXL04_023314|OH1004|CDS

CTGATCTTACTGCAAATCTCTGCGGTCATCCCCTACTCTGTGGCTTCCAGCAGGAATACCAGGCTGCCTTCTGATTCTGGTGCGTTTGCGGACTGGGTGGCTAATCCTTCGTCTTCCTCTGCTCTCAGAAATTCTGATCAGGACCTGTCGTTGGGCTTCAATGCCAGTGCCGCCGCCGCTGCGGTTGTTCACGGTGGAGGGTCGACCGGGATTTGGTCCACACCCTCTGCTCGACAGATCAACTATGGTGTTCCAGCTGA...

Protein

Download Protein FASTA

401 aa · LXL04_023314|LXL04_023314|OH1004|PROTEIN

MILLQISAVIPYSVASSRNTRLPSDSGAFADWVANPSSSSALRNSDQDLSLGFNASAAAAAVVHGGGSTGIWSTPSARQINYGVPAEMGMLVVAPSSHHLSDHGHAHSLNAPFSGTAVAATATALGVGVIPLITASPCLEEGMRGGRGNNANTTSNSIQFWQQHPHQSYLKKSIVPDHGFGGGGGGVGGSASTSGSTLTCQDCGNQAKKDCYHRRCRTCCKSRGFDCATHVKSTWVPAARRRERQLITSTGAAAGSSAST...

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_023314`
TK1151 ID	TkA02G401670
OH-1004 ID	LXL04_023314
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	57.400
Protein coverage (%)	TK1151 88.095 / OH-1004 24.688 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

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Basic Information and Functional Annotation

Gene ID LXL04_023314

Location Chr05:32100033-32101503 (-)

Description Similar to LRP1: Protein LATERAL ROOT PRIMORDIUM 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g12330`	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 Regulation of root elongation by histone acetylation in Arabidopsis.2009 · DOI: 10.1016/j.jmb.2008.09.040
`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
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_023314 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009299 mRNA transcription Biological Process

GO:0009555 pollen development Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009733 response to auxin 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:0048364 root development Biological Process

KEGG gene cross-reference

ath:AT1G19790

ath:AT1G75520

ath:AT5G12330

ath:AT5G66350

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.

Nucleus0.980

Rank 1 · LXL04_023314 · OH-1004

Cytoplasm0.078

Rank 2 · LXL04_023314 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_023314 · OH-1004

Endoplasmic reticulum0.018

Rank 4 · LXL04_023314 · OH-1004

Plastid0.010

Rank 5 · LXL04_023314 · 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.

PF05142.18DUF702197-353 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_023314	`PF05142.18`	DUF702	197	353	2.3e-59	201.0

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
`Q94CK9`	Arabidopsis thaliana	Protein LATERAL ROOT PRIMORDIUM 1	50.625%	Swiss-Prot	strong database homology
`Q9XGX0`	Arabidopsis thaliana	Protein SHORT INTERNODES	49.367%	Swiss-Prot	weak database homology
`Q9FXH7`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 7	41.935%	Swiss-Prot	moderate database homology
`Q9LQZ5`	Arabidopsis thaliana	Protein SHI RELATED SEQUENCE 5	46.961%	Swiss-Prot	weak database homology

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