LXL04_009584 | RubberDandelionOmics

Gene overview

LXL04_009584

Reference: OH-1004 Chr: Chr02 Coordinates: 129258534-129263824 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3648 bp · LXL04_009584|LXL04_009584|OH1004|cDNA

atgatgcgaaagataagtgaaaatacacatgggcatccattgaaggaccagaagttccctcaatcaggtaatacaacaccatgtacatcttgttctcttggaaagttaattgtaagaccctcaccagtaaaagttgaaagtgaatcacccagatttcttgaaagaattcaaggtgatatatgtggaccaattcatccaccatctgggccttttagatacttcatggtcctgatagatgcatccagcagatggtctcatgt...

CDS

Download CDS FASTA

3648 bp · LXL04_009584|LXL04_009584|OH1004|CDS

ATGATGCGAAAGATAAGTGAAAATACACATGGGCATCCATTGAAGGACCAGAAGTTCCCTCAATCAGGTAATACAACACCATGTACATCTTGTTCTCTTGGAAAGTTAATTGTAAGACCCTCACCAGTAAAAGTTGAAAGTGAATCACCCAGATTTCTTGAAAGAATTCAAGGTGATATATGTGGACCAATTCATCCACCATCTGGGCCTTTTAGATACTTCATGGTCCTGATAGATGCATCCAGCAGATGGTCTCATGT...

Protein

Download Protein FASTA

1215 aa · LXL04_009584|LXL04_009584|OH1004|PROTEIN

MMRKISENTHGHPLKDQKFPQSGNTTPCTSCSLGKLIVRPSPVKVESESPRFLERIQGDICGPIHPPSGPFRYFMVLIDASSRWSHVCLLSTRNMAFAKFLAQIIKLRAYFPDYAIKRVRLDNAGEFTSQSFNDYCMAVGIVVEHPVAHVHTQNGLAESLIKRLQLIARPLIMRTKLPVFIWGHAILHAVSLIRIRPSAYHTYSPLQLVFGQEPNISHLRIFGCAVYVPIAPPQRTKMGPQRRLGIYVGYETVSIIRYLE...

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_009584`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009584

Location Chr02:129258534-129263824 (+)

Description Similar to GIP: Copia protein

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
`At5g50100`	Uncharacterized protein At5g50100, chloroplastic.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009584 · 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:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

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

KEGG gene cross-reference

ath:AT5G50100

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Plastid0.440

Rank 1 · LXL04_009584 · OH-1004

Mitochondrion0.271

Rank 2 · LXL04_009584 · OH-1004

Cytoplasm0.172

Rank 3 · LXL04_009584 · OH-1004

Nucleus0.078

Rank 4 · LXL04_009584 · OH-1004

Peroxisome0.068

Rank 5 · LXL04_009584 · 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.

PF00665.33rve54-144 aa

PF25597.2SH3_retrovirus224-283 aa

PF07727.20RVT_2494-737 aa

PF04134.18DCC1-like1080-1190 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009584	`PF00665.33`	rve	54	144	1.8e-08	35.2
LXL04_009584	`PF25597.2`	SH3_retrovirus	224	283	2e-07	31.4
LXL04_009584	`PF07727.20`	RVT_2	494	737	8.7e-63	212.9
LXL04_009584	`PF04134.18`	DCC1-like	1080	1190	7.1e-25	89.2

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	33.084%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	32.480%	Swiss-Prot	weak database homology
`Q8W485`	Arabidopsis thaliana	Uncharacterized protein At5g50100, chloroplastic	63.452%	Swiss-Prot	weak database homology

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