LXL04_016552 | RubberDandelionOmics

Gene overview

LXL04_016552

Reference: OH-1004 Chr: Chr03 Coordinates: 126789795-126792008 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1158 bp · LXL04_016552|LXL04_016552|OH1004|cDNA

ATGGCGGGTTCAGGACCAACAGACAGAGGCAAAGAAGCTATAGGAATGTTGGCTCTTCACGAGACTCTCAGAAACCTCTGTATCAACTCCGATTGGACTTACTCTGTCTTCTGGACCATTCGTCCTCGCCCGCGACTTCGTGGTGGTAATGGGTGCAAAGTAGGAGACGACAATGGTAGCTTGATGTTGATGTGGGAAGATGGGTTTTGCAGAGGAGGAGTTGATGAAATGGATGGAGGTGAAGATCAAGTTAAGAAATC...

CDS

Download CDS FASTA

1158 bp · LXL04_016552|LXL04_016552|OH1004|CDS

ATGGCGGGTTCAGGACCAACAGACAGAGGCAAAGAAGCTATAGGAATGTTGGCTCTTCACGAGACTCTCAGAAACCTCTGTATCAACTCCGATTGGACTTACTCTGTCTTCTGGACCATTCGTCCTCGCCCGCGACTTCGTGGTGGTAATGGGTGCAAAGTAGGAGACGACAATGGTAGCTTGATGTTGATGTGGGAAGATGGGTTTTGCAGAGGAGGAGTTGATGAAATGGATGGAGGTGAAGATCAAGTTAAGAAATC...

Protein

Download Protein FASTA

385 aa · LXL04_016552|LXL04_016552|OH1004|PROTEIN

MAGSGPTDRGKEAIGMLALHETLRNLCINSDWTYSVFWTIRPRPRLRGGNGCKVGDDNGSLMLMWEDGFCRGGVDEMDGGEDQVKKSFSKMSIQLYNYGEGLMGKVASDKCHKWVFKEPSESEQNISNYWQSSFDAIPTEWTEQFDSGIQTIAVIQAGHGLLQLGSCKIIPEDLHFVLRMRHTFESLGYQSGFYLSQLFASTRANMSPPSTTTIPLKQLPIPTRPPPLYNWTPQRTVPSPNNFHHPGPLGYPQKDETHMF...

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_016552`
TK1151 ID	TkA02G124290
OH-1004 ID	LXL04_016552
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_016552

Location Chr03:126789795-126792008 (-)

Description Similar to RSS3: Protein RICE SALT SENSITIVE 3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g31280`	Transcription factor that may regulate root development.	No verified direct reference in this release
`At1g06150`	Transcription factor that may regulate root development.	No verified direct reference in this release
`At2g27230`	Transcription activator that regulates root development; promotes the production of stele cells in roots.	No verified direct reference in this release
`At1g64625`	Transcription factor that may regulate root development.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os11g0446000`	Involved in the repression of jasmonate (JA)-induced genes.	RICE SALT SENSITIVE3 forms a ternary complex with JAZ and class-C bHLH factors and regulates jasmonate-induced gene expression and root cell elongation.2013 · DOI: 10.1105/tpc.113.112052

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016552 · 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:0007140 male meiotic nuclear division Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0010089 xylem development Biological Process

GO:0010479 stele development Biological Process

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

GO:0048316 seed development Biological Process

GO:0048364 root development Biological Process

GO:0051321 meiotic cell cycle Biological Process

GO:0071365 cellular response to auxin stimulus Biological Process

GO:0090058 metaxylem development Biological Process

KEGG gene cross-reference

ath:AT1G06150

ath:AT1G64625

ath:AT2G27230

ath:AT2G31280

dosa:Os11g0446000

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.

Nucleus0.919

Rank 1 · LXL04_016552 · OH-1004

Cytoplasm0.121

Rank 2 · LXL04_016552 · OH-1004

Cell membrane0.061

Rank 3 · LXL04_016552 · OH-1004

Endoplasmic reticulum0.048

Rank 4 · LXL04_016552 · OH-1004

Plastid0.019

Rank 5 · LXL04_016552 · 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.

PF14215.13bHLH-MYC_N19-79 aa

PF14215.13bHLH-MYC_N85-184 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016552	`PF14215.13`	bHLH-MYC_N	19	79	7e-30	105.4
LXL04_016552	`PF14215.13`	bHLH-MYC_N	85	184	7e-30	105.4

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
`Q58G01`	Arabidopsis thaliana	Transcription factor bHLH155	33.136%	Swiss-Prot	weak database homology
`P0C7P8`	Arabidopsis thaliana	Transcription factor EMB1444	31.492%	Swiss-Prot	weak database homology
`Q9XIN0`	Arabidopsis thaliana	Transcription factor LHW	29.592%	Swiss-Prot	weak database homology
`Q7XJU0`	Arabidopsis thaliana	Transcription factor bHLH157	26.797%	Swiss-Prot	weak database homology
`K4PW38`	Oryza sativa subsp. japonica	Protein RICE SALT SENSITIVE 3	53.846%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card