LXL04_021588 | RubberDandelionOmics

Gene overview

LXL04_021588

Reference: OH-1004 Chr: Chr04 Coordinates: 132880644-132896911 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6657 bp · LXL04_021588|LXL04_021588|OH1004|cDNA

ATGCCGTCAATGGTGTATCCGGTATCGTTTGTCGCCGGAGACACTCCTCTGAAACTTGTCGATTTCTTCAAGATCGACGGAGTGTATAACCTCAGAAGCATATTCCCGATAAACCCCGCAACGGAATTAGCCCCTGGTTTGATTATTATCGGCGCTCAAGTGAATCAGCGAAGAACAGCCCCTGGTAATGTACCGTATAAAATATTCGAATCGACGAATAAGTGCTGCAGTACGGTCATTGCCGATTCTCCTGCAAAACC...

CDS

Download CDS FASTA

6657 bp · LXL04_021588|LXL04_021588|OH1004|CDS

ATGCCGTCAATGGTGTATCCGGTATCGTTTGTCGCCGGAGACACTCCTCTGAAACTTGTCGATTTCTTCAAGATCGACGGAGTGTATAACCTCAGAAGCATATTCCCGATAAACCCCGCAACGGAATTAGCCCCTGGTTTGATTATTATCGGCGCTCAAGTGAATCAGCGAAGAACAGCCCCTGGTAATGTACCGTATAAAATATTCGAATCGACGAATAAGTGCTGCAGTACGGTCATTGCCGATTCTCCTGCAAAACC...

Protein

Download Protein FASTA

2218 aa · LXL04_021588|LXL04_021588|OH1004|PROTEIN

MPSMVYPVSFVAGDTPLKLVDFFKIDGVYNLRSIFPINPATELAPGLIIIGAQVNQRRTAPGNVPYKIFESTNKCCSTVIADSPAKPFSVLPHFLANIFQDFVASNTPSSIHICNTSSKSKITATRSSSSSLHFEMNSQRLSLTPQKRSNESSEVGGFKRRTPDSLVVSSPDVSGSGRVYKLKILLPNGMTVLLKIPEGTEWITVKELANRAKNSYDRAVKKTSNPEKHVNWNADLYFLDDTDKRFSNSLKLTNLELNRV...

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_021588`
TK1151 ID	TkA05G408450
OH-1004 ID	LXL04_021588
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	98.600
Protein coverage (%)	TK1151 97.263 / OH-1004 72.182 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_021588

Location Chr04:132880644-132896911 (+)

Description Similar to GMI1: Structural maintenance of chromosomes flexible hinge domain-containing protein GMI1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g24280`	Contributes to DNA double-strand break (DSB) repair via somatic homologous recombination.	GMI1, a structural-maintenance-of-chromosomes-hinge domain-containing protein, is involved in somatic homologous recombination in Arabidopsis.2011 · DOI: 10.1111/j.1365-313x.2011.04604.x
`At3g49250`	Component of the RNA-directed DNA methylation (RdDM) machinery, probably by facilitating an RNAi-mediated epigenetic modification involving secondary siRNAs and spreading of DNA methylation, thus leading to gene silencing.	A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation.2008 · DOI: 10.1038/ng.119 RNA polymerase V transcription guides ARGONAUTE4 to chromatin.2009 · DOI: 10.1038/ng.365 IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana.2009 · DOI: 10.1038/nsmb.1690 RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats.2012 · DOI: 10.4161/epi.20290

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021588 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000724 double-strand break repair via homologous recombination Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

GO:0000419 RNA polymerase V complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0042803 protein homodimerization activity Molecular Function

KEGG gene cross-reference

ath:AT3G49250

ath:AT5G24280

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.

Nucleus0.501

Rank 1 · LXL04_021588 · OH-1004

Cytoplasm0.414

Rank 2 · LXL04_021588 · OH-1004

Cell membrane0.107

Rank 3 · LXL04_021588 · OH-1004

Endoplasmic reticulum0.066

Rank 4 · LXL04_021588 · OH-1004

Mitochondrion0.062

Rank 5 · LXL04_021588 · 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.

PF28659.1GMI1_N180-267 aa

PF13589.13HATPase_c_3295-412 aa

PF28657.1GMI1_middle716-853 aa

PF28626.1GMI1_Ig_1858-997 aa

PF28628.1GMI1_Ig_21002-1119 aa

PF28627.1GMI1_Ig_31123-1224 aa

PF28658.1GMI1_Ig_4th1228-1329 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021588	`PF28659.1`	GMI1_N	180	267	3.8e-20	72.8
LXL04_021588	`PF13589.13`	HATPase_c_3	295	412	1.6e-12	48.3
LXL04_021588	`PF28657.1`	GMI1_middle	716	853	3.1e-61	205.8
LXL04_021588	`PF28626.1`	GMI1_Ig_1	858	997	3e-53	179.9
LXL04_021588	`PF28628.1`	GMI1_Ig_2	1002	1119	1.4e-32	112.8
LXL04_021588	`PF28627.1`	GMI1_Ig_3	1123	1224	2e-35	121.5
LXL04_021588	`PF28658.1`	GMI1_Ig_4th	1228	1329	1.6e-37	128.3

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
`F4KFS5`	Arabidopsis thaliana	Structural maintenance of chromosomes flexible hinge domain-containing protein GMI1	41.708%	Swiss-Prot	moderate database homology
`Q94A79`	Arabidopsis thaliana	Protein DEFECTIVE IN MERISTEM SILENCING 3	49.292%	Swiss-Prot	weak database homology

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