LXL04_028445 | RubberDandelionOmics

Gene overview

LXL04_028445

Reference: OH-1004 Chr: Chr06 Coordinates: 41987313-41999894 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

9225 bp · LXL04_028445|LXL04_028445|OH1004|cDNA

atgtcaaaatctgattctcataatattgctttcaaccttgctagttctatcggatccaacagcagagctccgacattgtttcctgaggagtatgatgcttgggtaatccacatggaggattacatcaccgggatagagaaggttggaatggatgtctggtattctattaccgaaggaccgtacaaaaacaaaacctattgtcctactggaataaccaccattaaagagctaaaagagcttcaagaacttcatgctgatct...

CDS

Download CDS FASTA

9225 bp · LXL04_028445|LXL04_028445|OH1004|CDS

ATGTCAAAATCTGATTCTCATAATATTGCTTTCAACCTTGCTAGTTCTATCGGATCCAACAGCAGAGCTCCGACATTGTTTCCTGAGGAGTATGATGCTTGGGTAATCCACATGGAGGATTACATCACCGGGATAGAGAAGGTTGGAATGGATGTCTGGTATTCTATTACCGAAGGACCGTACAAAAACAAAACCTATTGTCCTACTGGAATAACCACCATTAAAGAGCTAAAAGAGCTTCAAGAACTTCATGCTGATCT...

Protein

Download Protein FASTA

3074 aa · LXL04_028445|LXL04_028445|OH1004|PROTEIN

MSKSDSHNIAFNLASSIGSNSRAPTLFPEEYDAWVIHMEDYITGIEKVGMDVWYSITEGPYKNKTYCPTGITTIKELKELQELHADLPSDHMLKDSYGSNELLDSIQSSLLAEYGAFKQSSDESIDKTSERFHQLLSRMEKYDLARKEVEKKTTFLQSLRAEFFNIGQTIRGHEQFKNYKMPEVLGILKAHEAELVKASKTNITLALVSKSEKQKKKEKKVSSTDSESEESDSDYEWTAEEKALMVHNPKKFFKKNYSKF...

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_028445`
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_028445

Location Chr06:41987313-41999894 (-)

Description Similar to GIP: Copia protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

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

View annotation sources

Functional annotation source: OH1004 · LXL04_028445 · 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.

Nucleus0.667

Rank 1 · LXL04_028445 · OH-1004

Cytoplasm0.330

Rank 2 · LXL04_028445 · OH-1004

Mitochondrion0.046

Rank 3 · LXL04_028445 · OH-1004

Cell membrane0.029

Rank 4 · LXL04_028445 · OH-1004

Endoplasmic reticulum0.019

Rank 5 · LXL04_028445 · 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.

PF22936.2Pol_BBD882-954 aa

PF13976.12gag_pre-integrs989-1059 aa

PF00665.33rve1074-1174 aa

PF29688.1TnsB_C1138-1194 aa

PF25597.2SH3_retrovirus1248-1303 aa

PF07727.20RVT_21544-1647 aa

PF07727.20RVT_21653-1712 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028445	`PF22936.2`	Pol_BBD	882	954	2.3e-19	70.2
LXL04_028445	`PF13976.12`	gag_pre-integrs	989	1059	8.4e-15	55.0
LXL04_028445	`PF00665.33`	rve	1074	1174	2.5e-14	54.1
LXL04_028445	`PF29688.1`	TnsB_C	1138	1194	1.1e-07	32.5
LXL04_028445	`PF25597.2`	SH3_retrovirus	1248	1303	4.7e-16	59.0
LXL04_028445	`PF07727.20`	RVT_2	1544	1647	9e-45	153.9
LXL04_028445	`PF07727.20`	RVT_2	1653	1712	9e-45	153.9

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
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	34.130%	Swiss-Prot	weak database homology
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	33.555%	Swiss-Prot	weak database homology
`P92519`	Arabidopsis thaliana	Uncharacterized mitochondrial protein AtMg00810	30.622%	Swiss-Prot	weak database homology

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