LXL04_036249 | RubberDandelionOmics

Gene overview

LXL04_036249

Reference: OH-1004 Chr: Chr08 Coordinates: 38575728-38586744 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5628 bp · LXL04_036249|LXL04_036249|OH1004|cDNA

ATGGCTACTGCAACTTCCTCTGATCCTGTAATGAAATCGGAGGGCAGTGCCAGTGGCGGTGAGACTTCTGAAGCGGCGTCGACGATTGGGATGGCGGCGGCCGCCGCGGTGGTAGTAAAGGGGAACAATTATCAGCAGCAGTTGATGGTGAAGTATAAAGGGATTAAGAAATCGAAGAAGGATAGAGGTTGTACGGCTAAAGAACGCATCAGTAAAATGCCTCCTTGTGCTGCTGGGAAACGTAGCTCTATCTACAGAGG...

CDS

Download CDS FASTA

5628 bp · LXL04_036249|LXL04_036249|OH1004|CDS

ATGGCTACTGCAACTTCCTCTGATCCTGTAATGAAATCGGAGGGCAGTGCCAGTGGCGGTGAGACTTCTGAAGCGGCGTCGACGATTGGGATGGCGGCGGCCGCCGCGGTGGTAGTAAAGGGGAACAATTATCAGCAGCAGTTGATGGTGAAGTATAAAGGGATTAAGAAATCGAAGAAGGATAGAGGTTGTACGGCTAAAGAACGCATCAGTAAAATGCCTCCTTGTGCTGCTGGGAAACGTAGCTCTATCTACAGAGG...

Protein

Download Protein FASTA

1875 aa · LXL04_036249|LXL04_036249|OH1004|PROTEIN

MATATSSDPVMKSEGSASGGETSEAASTIGMAAAAAVVVKGNNYQQQLMVKYKGIKKSKKDRGCTAKERISKMPPCAAGKRSSIYRGVTRHRWTGRYEAHLWDKSTWNQNQNKKGKQGAYDDEEAAARAYDLAALKYWGPGTLINFPVTDYTRDLEEMQNLTREDYLASLRRKGSGFSRGNSKCRGISSTRWDSPLGRGPDYDNRMHHGDETPTENEYVGGFRMDRKIDLTPYIKWWAPTKSRQAAEKSSDETNTNHASS...

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_036249`
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_036249

Location Chr08:38575728-38586744 (-)

Description Similar to Retrovirus-related Pol polyprotein from transposon TNT 1-94

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g41710`	Probably acts as a transcriptional activator.	No verified direct reference in this release
`UniProt: Q94HW2`	Retrovirus-related Pol polyprotein from transposon RE1.	No verified direct reference in this release
`At4g02960`	Retrovirus-related Pol polyprotein from transposon RE2.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0389000`	Transcription activator involved in the control of organ size.	A novel AP2-type transcription factor, SMALL ORGAN SIZE1, controls organ size downstream of an auxin signaling pathway.2014 · DOI: 10.1093/pcp/pcu023 SMALL ORGAN SIZE 1 and SMALL ORGAN SIZE 2/DWARF AND LOW-TILLERING Form a Complex to Integrate Auxin and Brassinosteroid Signaling in Rice.2017 · DOI: 10.1016/j.molp.2016.12.013 The RLA1/SMOS1 Transcription Factor Functions with OsBZR1 to Regulate Brassinosteroid Signaling and Rice Architecture.2017 · DOI: 10.1105/tpc.16.00611

Functional annotation source

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Functional annotation source: OH1004 · LXL04_036249 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006310 DNA recombination Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006508 proteolysis Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009742 brassinosteroid mediated signaling pathway Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0015074 DNA integration Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0003676 nucleic acid binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G41710

dosa:Os05g0389000

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.

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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.

Nucleus0.508

Rank 1 · LXL04_036249 · OH-1004

Cytoplasm0.449

Rank 2 · LXL04_036249 · OH-1004

Mitochondrion0.056

Rank 3 · LXL04_036249 · OH-1004

Cell membrane0.042

Rank 4 · LXL04_036249 · OH-1004

Endoplasmic reticulum0.039

Rank 5 · LXL04_036249 · 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.

PF00847.27AP285-139 aa

PF14244.13Retrotran_gag_3519-566 aa

PF13976.12gag_pre-integrs958-1002 aa

PF00665.33rve1019-1116 aa

PF07727.20RVT_21404-1531 aa

PF07727.20RVT_21534-1598 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036249	`PF00847.27`	AP2	85	139	3e-07	31.4
LXL04_036249	`PF14244.13`	Retrotran_gag_3	519	566	7.9e-09	35.9
LXL04_036249	`PF13976.12`	gag_pre-integrs	958	1002	2.8e-07	30.9
LXL04_036249	`PF00665.33`	rve	1019	1116	4.1e-12	47.0
LXL04_036249	`PF07727.20`	RVT_2	1404	1531	1.9e-48	165.9
LXL04_036249	`PF07727.20`	RVT_2	1534	1598	1.9e-48	165.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8GWK2`	Arabidopsis thaliana	AP2-like ethylene-responsive transcription factor At2g41710	57.816%	Swiss-Prot	weak database homology
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	36.803%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	35.075%	Swiss-Prot	weak database homology
`X5HYT8`	Oryza sativa subsp. japonica	AP2-like ethylene-responsive transcription factor SMOS1	49.459%	Swiss-Prot	weak database homology

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