LXL04_001948 | RubberDandelionOmics

Gene overview

LXL04_001948

Reference: OH-1004 Chr: Chr01 Coordinates: 37809874-37813474 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2247 bp · LXL04_001948|LXL04_001948|OH1004|cDNA

ATGGGTAGACCGCCCAGTAATGGAGGCCCTTCTTTCCGCTTTAACCCGGCCGAGaTTGCGGAGATGGAAGCCATCTTGCAAGCACACAAAACCCAAATGCCTGCACGTGAGGTTCTTGTTGCCTTAGCCGAAAAGTTCAGCAACTCTGAAGAACGAAAGGGAAAGATTGAAGTTCAAATGAAACAAGTATGGAATTGGTTCCAAAATAGACGATATGCAATCAGGGCTAAAGCAGGAAAATCACCAGGGAAGTTAATAAA...

CDS

Download CDS FASTA

2247 bp · LXL04_001948|LXL04_001948|OH1004|CDS

ATGGGTAGACCGCCCAGTAATGGAGGCCCTTCTTTCCGCTTTAACCCGGCCGAGATTGCGGAGATGGAAGCCATCTTGCAAGCACACAAAACCCAAATGCCTGCACGTGAGGTTCTTGTTGCCTTAGCCGAAAAGTTCAGCAACTCTGAAGAACGAAAGGGAAAGATTGAAGTTCAAATGAAACAAGTATGGAATTGGTTCCAAAATAGACGATATGCAATCAGGGCTAAAGCAGGAAAATCACCAGGGAAGTTAATAAA...

Protein

Download Protein FASTA

748 aa · LXL04_001948|LXL04_001948|OH1004|PROTEIN

MGRPPSNGGPSFRFNPAEIAEMEAILQAHKTQMPAREVLVALAEKFSNSEERKGKIEVQMKQVWNWFQNRRYAIRAKAGKSPGKLINITQVNRDDNPTMAKGIPQPTLPHAASAATVRFMPQAQQHPTVPTVRTFPQAPQNTMSFSVQNAGRVTDNSQMEYEAKSARDGAWYDVSTFLSHRSLDSGDPEVMVRFAGFGAEEDEWVNVRKNVRQRSLPCEASECVAVLPADLILCFQEGKEQALYFDAHVLDAQRRRHDVR...

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_001948`
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_001948

Location Chr01:37809874-37813474 (+)

Description Similar to SHH2: Protein SAWADEE HOMEODOMAIN HOMOLOG 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g18380`	May play a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM.	No verified direct reference in this release
`At1g15215`	Involved in RNA-directed DNA methylation (RdDM).	SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.2011 · DOI: 10.1371/journal.pgen.1002195 An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing.2011 · DOI: 10.1038/cr.2011.173 Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.2013 · DOI: 10.1038/nature12178 DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.2013 · DOI: 10.1073/pnas.1300585110

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001948 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0007155 cell adhesion Biological Process

GO:0007339 binding of sperm to zona pellucida Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:2000359 regulation of binding of sperm to zona pellucida Biological Process

GO:0005615 extracellular space Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0031012 extracellular matrix Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

KEGG gene cross-reference

ath:AT1G15215

ath:AT3G18380

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.

Nucleus0.870

Rank 1 · LXL04_001948 · OH-1004

Cytoplasm0.182

Rank 2 · LXL04_001948 · OH-1004

Cell membrane0.040

Rank 3 · LXL04_001948 · OH-1004

Endoplasmic reticulum0.030

Rank 4 · LXL04_001948 · OH-1004

Mitochondrion0.021

Rank 5 · LXL04_001948 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF16719.12SAWADEE158-285 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001948	`PF16719.12`	SAWADEE	158	285	3e-44	150.8

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
`Q8RWJ7`	Arabidopsis thaliana	Protein SAWADEE HOMEODOMAIN HOMOLOG 2	64.821%	Swiss-Prot	weak database homology
`Q9XI47`	Arabidopsis thaliana	Protein SAWADEE HOMEODOMAIN HOMOLOG 1	38.989%	Swiss-Prot	weak database homology

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