LXL04_007880 | RubberDandelionOmics

Gene overview

LXL04_007880

Reference: OH-1004 Chr: Chr02 Coordinates: 70000060-70002717 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2643 bp · LXL04_007880|LXL04_007880|OH1004|cDNA

atgtgcatcgactatcgggaactgaataaactaacagtgaaaaaccgataccccttacccagaatagatgatctatttgaccaactccaagggtcaactcacttttcaaaaatagatctgaggtcaggatACCATCAACTTAAAGTCCAGGGAGAAGACAtccctaaaacggcatttcgaactcgctacgggcactacgagttcctagtcatgccatttggattgaccaatgcaccagcagtattcatggatctcatgaa...

CDS

Download CDS FASTA

2643 bp · LXL04_007880|LXL04_007880|OH1004|CDS

ATGTGCATCGACTATCGGGAACTGAATAAACTAACAGTGAAAAACCGATACCCCTTACCCAGAATAGATGATCTATTTGACCAACTCCAAGGGTCAACTCACTTTTCAAAAATAGATCTGAGGTCAGGATACCATCAACTTAAAGTCCAGGGAGAAGACATCCCTAAAACGGCATTTCGAACTCGCTACGGGCACTACGAGTTCCTAGTCATGCCATTTGGATTGACCAATGCACCAGCAGTATTCATGGATCTCATGAA...

Protein

Download Protein FASTA

880 aa · LXL04_007880|LXL04_007880|OH1004|PROTEIN

MCIDYRELNKLTVKNRYPLPRIDDLFDQLQGSTHFSKIDLRSGYHQLKVQGEDIPKTAFRTRYGHYEFLVMPFGLTNAPAVFMDLMNRVCRPYLDKFVIVFIDDILIYSRSKEEHGRHLRLILELLRKEKLYAKFSKCEFWINEVKFLGHVVSKDGIHVDPSKIEEIKNWKAPTTPTEIRQFLGLAGYYRRFIANFSKLAKPLTTLTQKDVSFNWRDKQEASFQKLKHMLCSAPILSLPEGTEDFVVYCDASNQGLGCVL...

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_007880`
TK1151 ID	TkA03G122020
OH-1004 ID	LXL04_007880
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	93.800
Protein coverage (%)	TK1151 99.672 / OH-1004 34.545 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_007880`
Location	Chr02:70000060-70002717 (+)
Description	Similar to TY3B-I: Transposon Ty3-I Gag-Pol polyprotein (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Arabidopsis / Rice Reference Genes and Papers	Download references for this gene Arabidopsis No hit for this species in the current source table. Rice No hit for this species in the current source table.
Functional annotation source	View annotation sources Functional annotation source: OH1004 · `LXL04_007880` · 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:0075523 viral translational frameshifting Biological Process GO:0005634 nucleus Cellular Component GO:0005737 cytoplasm Cellular Component GO:0003677 DNA binding Molecular Function GO:0003723 RNA binding Molecular Function GO:0003887 DNA-directed DNA polymerase activity 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
KEGG gene cross-reference	sce:YGR109W-B sce:YIL082W-A spo:2538755 spo:2541833 spo:2541991 spo:3361422 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.

Cytoplasm0.535

Rank 1 · LXL04_007880 · OH-1004

Nucleus0.348

Rank 2 · LXL04_007880 · OH-1004

Mitochondrion0.156

Rank 3 · LXL04_007880 · OH-1004

Cell membrane0.040

Rank 4 · LXL04_007880 · OH-1004

Peroxisome0.029

Rank 5 · LXL04_007880 · 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.

PF00078.33RVT_12-151 aa

PF17919.8RT_RNaseH_2215-309 aa

PF17917.8RT_RNaseH242-339 aa

PF17921.8Integrase_H2C2431-484 aa

PF00665.33rve508-599 aa

PF29688.1TnsB_C552-617 aa

PF31073.1DUF8803718-785 aa

PF24626.2SH3_Tf2-1721-785 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007880	`PF00078.33`	RVT_1	2	151	2.1e-36	126.4
LXL04_007880	`PF17919.8`	RT_RNaseH_2	215	309	1.4e-30	106.0
LXL04_007880	`PF17917.8`	RT_RNaseH	242	339	5.8e-34	117.1
LXL04_007880	`PF17921.8`	Integrase_H2C2	431	484	1.4e-16	61.1
LXL04_007880	`PF00665.33`	rve	508	599	2.2e-08	35.0
LXL04_007880	`PF29688.1`	TnsB_C	552	617	4.1e-06	27.4
LXL04_007880	`PF31073.1`	DUF8803	718	785	8.9e-07	29.4
LXL04_007880	`PF24626.2`	SH3_Tf2-1	721	785	1.1e-27	96.6

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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