LXL04_020120 | RubberDandelionOmics

Gene overview

LXL04_020120

Reference: OH-1004 Chr: Chr04 Coordinates: 52519086-52526575 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3681 bp · LXL04_020120|LXL04_020120|OH1004|cDNA

ATGTCGTCCTCTGTTCCTGTCGAGGTGATCGACGACGACGACGATTTTGATTGGGATGCAGCCGTTAGAGAGATTGATGCCGCTTGTGGTGCAGCCACTACACTATCTTCATCTGGTGTTACTTCTACTAGCGCACCCATATATCGAAATGCTAATATACATACGGGTTCTTGCCCTAAGACAGAAAACAACAAACCCGCTTCGTCTCGTCAATCCACACTTGATAGATTCGTTGGATTGACAGGCTTGAAATCAGCCAA...

CDS

Download CDS FASTA

3681 bp · LXL04_020120|LXL04_020120|OH1004|CDS

ATGTCGTCCTCTGTTCCTGTCGAGGTGATCGACGACGACGACGATTTTGATTGGGATGCAGCCGTTAGAGAGATTGATGCCGCTTGTGGTGCAGCCACTACACTATCTTCATCTGGTGTTACTTCTACTAGCGCACCCATATATCGAAATGCTAATATACATACGGGTTCTTGCCCTAAGACAGAAAACAACAAACCCGCTTCGTCTCGTCAATCCACACTTGATAGATTCGTTGGATTGACAGGCTTGAAATCAGCCAA...

Protein

Download Protein FASTA

1226 aa · LXL04_020120|LXL04_020120|OH1004|PROTEIN

MSSSVPVEVIDDDDDFDWDAAVREIDAACGAATTLSSSGVTSTSAPIYRNANIHTGSCPKTENNKPASSRQSTLDRFVGLTGLKSANQDVRHDAQDKVECNDEISSSVSIDPEAAKTWIYPVAESIPVRDYQASITKTALFSNTLVSLPTGLGKTLIAAVVMYNYYRWFPEDLMWCSISGKIVFAAPSRPLVTQQIEACHKIVGIPQEYTVDMTGQICPSKRADIWKKKRIFFLTPQVLDHDIDSGTCDMKKLVCLVLDE...

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_020120`
TK1151 ID	TkA05G140380
OH-1004 ID	LXL04_020120
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.400
Protein coverage (%)	TK1151 100.000 / OH-1004 25.204 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_020120

Location Chr04:52519086-52526575 (+)

Description Similar to FANCM: DEAD-box ATP-dependent RNA helicase FANCM

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g35530`	Involved in ordered homologous recombination (HR) events in somatic and meiotic cells.	The Fanconi anemia ortholog FANCM ensures ordered homologous recombination in both somatic and meiotic cells in Arabidopsis.2012 · DOI: 10.1105/tpc.112.096644 FANCM limits meiotic crossovers.2012 · DOI: 10.1126/science.1220381 The requirement for recombination factors differs considerably between different pathways of homologous double-strand break repair in somatic plant cells.2012 · DOI: 10.1111/j.1365-313x.2012.05119.x MHF1 plays Fanconi anaemia complementation group M protein (FANCM)-dependent and FANCM-independent roles in DNA repair and homologous recombination in plants.2014 · DOI: 10.1111/tpj.12507 FANCM-associated proteins MHF1 and MHF2, but not the other Fanconi anemia factors, limit meiotic crossovers.2014 · DOI: 10.1093/nar/gku614 AAA-ATPase FIDGETIN-LIKE 1 and Helicase FANCM Antagonize Meiotic Crossovers by Distinct Mechanisms.2015 · DOI: 10.1371/journal.pgen.1005369

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_020120 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000712 resolution of meiotic recombination intermediates Biological Process

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

GO:0006281 DNA repair Biological Process

GO:0031297 replication fork processing Biological Process

GO:0035825 homologous recombination Biological Process

GO:0036297 interstrand cross-link repair Biological Process

GO:0045003 double-strand break repair via synthesis-dependent strand annealing Biological Process

GO:0045128 negative regulation of reciprocal meiotic recombination Biological Process

GO:0051321 meiotic cell cycle Biological Process

GO:1902527 positive regulation of protein monoubiquitination Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G35530

gga:100857997

hsa:57697

mmu:104806

ncr:NCU09318

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.

Nucleus0.923

Rank 1 · LXL04_020120 · OH-1004

Cytoplasm0.155

Rank 2 · LXL04_020120 · OH-1004

Mitochondrion0.026

Rank 3 · LXL04_020120 · OH-1004

Cell membrane0.022

Rank 4 · LXL04_020120 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_020120 · 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.

PF04851.22ResIII127-293 aa

PF00270.36DEAD130-299 aa

PF00271.38Helicase_C475-590 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_020120	`PF04851.22`	ResIII	127	293	6.8e-16	59.3
LXL04_020120	`PF00270.36`	DEAD	130	299	6.3e-21	75.5
LXL04_020120	`PF00271.38`	Helicase_C	475	590	8.3e-20	71.8

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
`I3XHK1`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase FANCM	45.408%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card