LXL04_027480 | RubberDandelionOmics

Gene overview

LXL04_027480

Reference: OH-1004 Chr: Chr06 Coordinates: 16905305-16923923 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6471 bp · LXL04_027480|LXL04_027480|OH1004|cDNA

ATGCATGCCATCGTTTATGTGTTCCAGAGGCTAAGGGAAGAGAGAAACAGAAAAACTCACCGGAAGGAAGGAGCCAAATGGtgttggtcgccggcaggaacaAAGACGTCGCCGGAAAATGTCTACTCGCCGGTAATGATCATTAACCCACTAACAGCCGCGGGAAGAAGAAAACACGTTCCAATGGTTTCTAACGGCCCTACACATCGAGAGGAAGATAAAAGAGGAGGAATTACTCATCGGAAAATCAGAAACCAGAG...

CDS

Download CDS FASTA

6471 bp · LXL04_027480|LXL04_027480|OH1004|CDS

ATGCATGCCATCGTTTATGTGTTCCAGAGGCTAAGGGAAGAGAGAAACAGAAAAACTCACCGGAAGGAAGGAGCCAAATGGTGTTGGTCGCCGGCAGGAACAAAGACGTCGCCGGAAAATGTCTACTCGCCGGTAATGATCATTAACCCACTAACAGCCGCGGGAAGAAGAAAACACGTTCCAATGGTTTCTAACGGCCCTACACATCGAGAGGAAGATAAAAGAGGAGGAATTACTCATCGGAAAATCAGAAACCAGAG...

Protein

Download Protein FASTA

2156 aa · LXL04_027480|LXL04_027480|OH1004|PROTEIN

MHAIVYVFQRLREERNRKTHRKEGAKWCWSPAGTKTSPENVYSPVMIINPLTAAGRRKHVPMVSNGPTHREEDKRGGITHRKIRNQRSSDGGRWQNTAAALLLRCCSLTGTREGRRRSPFIVGIELLNAGKNEGSGRLARVGLEHVGIDGWPDLISREGEQWLRLGFLGLVSREEEERRAGGLNGPFMQLPRISPAALQLSSFWQENPLNPQLTQMLLLTQQIDFNNKQAGRRWRKKNEIAPIDHSSLQSTIDLWRRRRK...

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_027480`
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_027480

Location Chr06:16905305-16923923 (-)

Description Similar to RE1: Retrovirus-related Pol polyprotein from transposon RE1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`UniProt: P92520`	Uncharacterized mitochondrial protein AtMg00820.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_027480 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006310 DNA recombination Biological Process

GO:0006508 proteolysis Biological Process

GO:0015074 DNA integration Biological Process

GO:0003676 nucleic acid binding Molecular Function

GO:0003964 RNA-directed DNA polymerase activity Molecular Function

GO:0004190 aspartic-type endopeptidase activity Molecular Function

GO:0004519 endonuclease activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference No functional description available

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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.

Cytoplasm0.504

Rank 1 · LXL04_027480 · OH-1004

Nucleus0.428

Rank 2 · LXL04_027480 · OH-1004

Mitochondrion0.070

Rank 3 · LXL04_027480 · OH-1004

Cell membrane0.053

Rank 4 · LXL04_027480 · OH-1004

Endoplasmic reticulum0.053

Rank 5 · LXL04_027480 · 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.

PF14244.13Retrotran_gag_3444-491 aa

PF14223.15Retrotran_gag_2475-651 aa

PF22936.2Pol_BBD789-863 aa

PF13976.12gag_pre-integrs899-962 aa

PF25597.2SH3_retrovirus1017-1051 aa

PF07727.20RVT_21233-1344 aa

PF13976.12gag_pre-integrs2024-2073 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027480	`PF14244.13`	Retrotran_gag_3	444	491	1.2e-08	35.3
LXL04_027480	`PF14223.15`	Retrotran_gag_2	475	651	3.3e-12	47.2
LXL04_027480	`PF22936.2`	Pol_BBD	789	863	2.1e-12	47.9
LXL04_027480	`PF13976.12`	gag_pre-integrs	899	962	2.4e-17	63.2
LXL04_027480	`PF25597.2`	SH3_retrovirus	1017	1051	3.5e-07	30.6
LXL04_027480	`PF07727.20`	RVT_2	1233	1344	8.1e-33	114.7
LXL04_027480	`PF13976.12`	gag_pre-integrs	2024	2073	2.4e-17	63.2

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
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	45.238%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	45.455%	Swiss-Prot	weak database homology
`P92520`	Arabidopsis thaliana	Uncharacterized mitochondrial protein AtMg00820	48.485%	Swiss-Prot	weak database homology

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