LXL04_006114 | RubberDandelionOmics

Gene overview

LXL04_006114

Reference: OH-1004 Chr: Chr02 Coordinates: 1941125-1950954 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3639 bp · LXL04_006114|LXL04_006114|OH1004|cDNA

ATGGATTCGTACTCGCTTAAGTGTGTCTCAGATCTACCTGATCCTTTCCGTGCAACTTTTAGTTTCAGGTATTTCAACTCGCTGCAGAGTGAATGCTTTTCAGCTTGTTTCCACTCCGACATCAACATGGTTATCTCAGCACCAACCGGCAGTGGGAAGACAGTGCTTTTTGAATTATCCATATTGCGGCTTCTATCTAAGTTCATCTCCCATGAAGGAAGATTTAATCATACGAAGGGAACTCTGAAAACAATATATAT...

CDS

Download CDS FASTA

3639 bp · LXL04_006114|LXL04_006114|OH1004|CDS

ATGGATTCGTACTCGCTTAAGTGTGTCTCAGATCTACCTGATCCTTTCCGTGCAACTTTTAGTTTCAGGTATTTCAACTCGCTGCAGAGTGAATGCTTTTCAGCTTGTTTCCACTCCGACATCAACATGGTTATCTCAGCACCAACCGGCAGTGGGAAGACAGTGCTTTTTGAATTATCCATATTGCGGCTTCTATCTAAGTTCATCTCCCATGAAGGAAGATTTAATCATACGAAGGGAACTCTGAAAACAATATATAT...

Protein

Download Protein FASTA

1212 aa · LXL04_006114|LXL04_006114|OH1004|PROTEIN

MDSYSLKCVSDLPDPFRATFSFRYFNSLQSECFSACFHSDINMVISAPTGSGKTVLFELSILRLLSKFISHEGRFNHTKGTLKTIYISPSKALVQEKLRSWNQKLGSWGINCLELTGDNESYSIKNIQDADIVLTTPEKFDAVTRFGIKDGGLSFFSDISLVLIDEVHLLNDPRGAALEAIVSRIKMIGRSPQMEKTPLAHVRFLAVSATIPNIDDLAEWLMVPVQGIKRFGEEMRPVKLTTKVFGYTPAKNDFLFEKAS...

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_006114`
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_006114

Location Chr02:1941125-1950954 (+)

Description Similar to MER3: DExH-box ATP-dependent RNA helicase DExH17

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g27730`	DNA helicase required for crossover formation, complete synapsis of homologous chromosomes and bivalent formation during meiosis.	Two meiotic crossover classes cohabit in Arabidopsis: one is dependent on MER3,whereas the other one is not.2005 · DOI: 10.1016/j.cub.2005.02.056 The Arabidopsis ROCK-N-ROLLERS gene encodes a homolog of the yeast ATP-dependent DNA helicase MER3 and is required for normal meiotic crossover formation.2005 · DOI: 10.1111/j.1365-313x.2005.02461.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0617500`	DNA helicase required for crossover formation, complete synapsis of homologous chromosomes and bivalent formation during meiosis.	MER3 is required for normal meiotic crossover formation, but not for presynaptic alignment in rice.2009 · DOI: 10.1242/jcs.049080 ZIP4 in homologous chromosome synapsis and crossover formation in rice meiosis.2012 · DOI: 10.1242/jcs.090993

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006114 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000712 resolution of meiotic recombination intermediates Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0051026 chiasma assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005694 chromosome Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0003676 nucleic acid binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003678 DNA helicase activity Molecular Function

GO:0005524 ATP binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT3G27730

dosa:Os02g0617500

hsa:164045

mmu:330149

xtr:779837

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.

Nucleus0.797

Rank 1 · LXL04_006114 · OH-1004

Cytoplasm0.223

Rank 2 · LXL04_006114 · OH-1004

Mitochondrion0.064

Rank 3 · LXL04_006114 · OH-1004

Cell membrane0.025

Rank 4 · LXL04_006114 · OH-1004

Endoplasmic reticulum0.013

Rank 5 · LXL04_006114 · 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.

PF00270.36DEAD27-216 aa

PF04851.22ResIII38-181 aa

PF00271.38Helicase_C343-425 aa

PF23445.2WHD_SNRNP200457-535 aa

PF02889.22Sec63546-861 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006114	`PF00270.36`	DEAD	27	216	5.4e-29	101.8
LXL04_006114	`PF04851.22`	ResIII	38	181	8.4e-08	33.0
LXL04_006114	`PF00271.38`	Helicase_C	343	425	1e-12	49.0
LXL04_006114	`PF23445.2`	WHD_SNRNP200	457	535	1.1e-11	45.4
LXL04_006114	`PF02889.22`	Sec63	546	861	9.4e-41	140.4

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
`Q5D892`	Arabidopsis thaliana	ATP-dependent DNA helicase homolog MER3	68.431%	Swiss-Prot	strong database homology
`B6DMK2`	Oryza sativa subsp. japonica	ATP-dependent DNA helicase MER3 homolog	56.544%	Swiss-Prot	strong database homology

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