LXL04_022439 | RubberDandelionOmics

Gene overview

LXL04_022439

Reference: OH-1004 Chr: Chr04 Coordinates: 150376304-150380488 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2850 bp · LXL04_022439|LXL04_022439|OH1004|cDNA

ATGAAAGGAGGTTCTTCTGGAAAGAAAAAAGGAGCTTCCCGGAGTCAAGATCATGGCTTTGCAGAGTTGATCTTCTCATGGTCTTTCGACGACATAGTCAACGACGGCCTTTACGAACACCAGGTGGAGAAAATACCACTTACTTTCCAGTCTGAAGAACACTATTTCCGTTCTTTTGTTTATCCATTGCTAGAGGAAACACGTACTGAATTAGCTTCCACTATGAAGATGATGTACAGAGCTCCATTTGCAGAGATTTC...

CDS

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2850 bp · LXL04_022439|LXL04_022439|OH1004|CDS

ATGAAAGGAGGTTCTTCTGGAAAGAAAAAAGGAGCTTCCCGGAGTCAAGATCATGGCTTTGCAGAGTTGATCTTCTCATGGTCTTTCGACGACATAGTCAACGACGGCCTTTACGAACACCAGGTGGAGAAAATACCACTTACTTTCCAGTCTGAAGAACACTATTTCCGTTCTTTTGTTTATCCATTGCTAGAGGAAACACGTACTGAATTAGCTTCCACTATGAAGATGATGTACAGAGCTCCATTTGCAGAGATTTC...

Protein

Download Protein FASTA

949 aa · LXL04_022439|LXL04_022439|OH1004|PROTEIN

MKGGSSGKKKGASRSQDHGFAELIFSWSFDDIVNDGLYEHQVEKIPLTFQSEEHYFRSFVYPLLEETRTELASTMKMMYRAPFAEISSLRKAKGKEKMMYDVTVGDWRNSECRKELYRTLPGDLLILANGEPGSLSDLQSSKWAFLLVNNTEDDDGTPVQFKVTASQEIEIHDGMFVVFLMNITTQKRIWNSLHKHANLDIIKEILYPDSMVKEQCDECSLGCNNPIQRFDPSLVSKLNESQKAAIMAAIHKMECSHKSS...

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_022439`
TK1151 ID	TkA05G468580
OH-1004 ID	LXL04_022439
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	98.900
Protein coverage (%)	TK1151 91.781 / OH-1004 91.781 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_022439

Location Chr04:150376304-150380488 (+)

Description Similar to MAA3: Probable helicase MAGATAMA 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g15570`	Probable helicase that may regulate RNA molecules involved in nucleolar organization and pollen tube guidance.	Attractive and repulsive interactions between female and male gametophytes in Arabidopsis pollen tube guidance.2000 · DOI: 10.1242/dev.127.20.4511 MAA3 (MAGATAMA3) helicase gene is required for female gametophyte development and pollen tube guidance in Arabidopsis thaliana.2008 · DOI: 10.1093/pcp/pcn130

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022439 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0006283 transcription-coupled nucleotide-excision repair Biological Process

GO:0006353 DNA-templated transcription termination Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0006386 termination of RNA polymerase III transcription Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006399 tRNA metabolic process Biological Process

GO:0006974 DNA damage response Biological Process

GO:0008033 tRNA processing Biological Process

GO:0009553 embryo sac development Biological Process

KEGG gene cross-reference

ath:AT4G15570

ddi:DDB_G0288923

sce:YLR430W

spo:2540523

spo:2541556

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.

Nucleus0.673

Rank 1 · LXL04_022439 · OH-1004

Cytoplasm0.330

Rank 2 · LXL04_022439 · OH-1004

Cell membrane0.049

Rank 3 · LXL04_022439 · OH-1004

Endoplasmic reticulum0.036

Rank 4 · LXL04_022439 · OH-1004

Mitochondrion0.034

Rank 5 · LXL04_022439 · 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.

PF20073.6DUF646917-213 aa

PF13086.13AAA_11237-440 aa

PF13245.13AAA_19258-600 aa

PF13086.13AAA_11529-605 aa

PF13087.13AAA_12612-808 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022439	`PF20073.6`	DUF6469	17	213	8.8e-70	235.2
LXL04_022439	`PF13086.13`	AAA_11	237	440	4.3e-34	119.2
LXL04_022439	`PF13245.13`	AAA_19	258	600	3.3e-09	37.7
LXL04_022439	`PF13086.13`	AAA_11	529	605	4.3e-34	119.2
LXL04_022439	`PF13087.13`	AAA_12	612	808	1.3e-59	201.8

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
`B6SFA4`	Arabidopsis thaliana	Probable helicase MAGATAMA 3	35.484%	Swiss-Prot	weak database homology

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