LXL04_017977 | RubberDandelionOmics

Gene overview

LXL04_017977

Reference: OH-1004 Chr: Chr04 Coordinates: 4524153-4538540 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

8016 bp · LXL04_017977|LXL04_017977|OH1004|cDNA

ATGGCAGGCCCCGATGGCAAGGAAGGAGAAGGATCAGGCAGTGCCAACACCACACCAAACTTTGATTCACCTTACTACATCCATCCCTCCGATTACCCCCGTCAATTACACGTTAACGATGTCCTTACTGATGGAAACTATGGTGACTGGTCGCAAGAGATGTTAAACTTCTTGTTTGCCAAAAACAAAATTGGTTTCATTGATGGAACCAGACAAAAGCCAGCTGCTAACTCTACTGAATACATGCCCTGGATGAGAAG...

CDS

Download CDS FASTA

8016 bp · LXL04_017977|LXL04_017977|OH1004|CDS

ATGGCAGGCCCCGATGGCAAGGAAGGAGAAGGATCAGGCAGTGCCAACACCACACCAAACTTTGATTCACCTTACTACATCCATCCCTCCGATTACCCCCGTCAATTACACGTTAACGATGTCCTTACTGATGGAAACTATGGTGACTGGTCGCAAGAGATGTTAAACTTCTTGTTTGCCAAAAACAAAATTGGTTTCATTGATGGAACCAGACAAAAGCCAGCTGCTAACTCTACTGAATACATGCCCTGGATGAGAAG...

Protein

Download Protein FASTA

2671 aa · LXL04_017977|LXL04_017977|OH1004|PROTEIN

MAGPDGKEGEGSGSANTTPNFDSPYYIHPSDYPRQLHVNDVLTDGNYGDWSQEMLNFLFAKNKIGFIDGTRQKPAANSTEYMPWMRSDAMIKGWLNTAMEKDIRTSVKYAATSQEIWEDLKERFGKESAPKAYELKQSLSATRQDGLSVSAYYTKLRGIWDEIHSVLPMPICECKRCTCDIGKKLSARQDKKRLYEFLLGLDAEFSTIRTQILAMQPIPTLGASYHLVVEDEQQRAISGSRRTEMDAAAFQAFHPNRHGY...

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_017977`
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_017977

Location Chr04:4524153-4538540 (+)

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
`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: P92519`	Uncharacterized mitochondrial protein AtMg00810.	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_017977 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006508 proteolysis Biological Process

GO:0015074 DNA integration Biological Process

GO:0071897 DNA biosynthetic process Biological Process

GO:0042575 DNA polymerase complex Cellular Component

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:0005524 ATP binding 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.

Cytoplasm0.586

Rank 1 · LXL04_017977 · OH-1004

Nucleus0.397

Rank 2 · LXL04_017977 · OH-1004

Cell membrane0.055

Rank 3 · LXL04_017977 · OH-1004

Plastid0.054

Rank 4 · LXL04_017977 · OH-1004

Endoplasmic reticulum0.052

Rank 5 · LXL04_017977 · 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.

PF14244.13Retrotran_gag_328-75 aa

PF14223.15Retrotran_gag_258-164 aa

PF22936.2Pol_BBD333-406 aa

PF00665.33rve512-608 aa

PF29688.1TnsB_C573-622 aa

PF25597.2SH3_retrovirus682-742 aa

PF07727.20RVT_2933-1175 aa

PF00078.33RVT_11953-2211 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017977	`PF14244.13`	Retrotran_gag_3	28	75	7e-10	39.3
LXL04_017977	`PF14223.15`	Retrotran_gag_2	58	164	1.1e-08	35.8
LXL04_017977	`PF22936.2`	Pol_BBD	333	406	2.1e-16	60.7
LXL04_017977	`PF00665.33`	rve	512	608	6.1e-12	46.4
LXL04_017977	`PF29688.1`	TnsB_C	573	622	1.5e-06	28.8
LXL04_017977	`PF25597.2`	SH3_retrovirus	682	742	2.2e-20	72.9
LXL04_017977	`PF07727.20`	RVT_2	933	1175	4.4e-74	249.9
LXL04_017977	`PF00078.33`	RVT_1	1953	2211	2.6e-31	109.8
LXL04_017977	`PF13966.12`	zf-RVT	2503	2571	7.6e-16	59.3

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	42.967%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	42.197%	Swiss-Prot	weak database homology
`P92519`	Arabidopsis thaliana	Uncharacterized mitochondrial protein AtMg00810	43.750%	Swiss-Prot	weak database homology

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