LXL04_022971 | RubberDandelionOmics

Gene overview

LXL04_022971

Reference: OH-1004 Chr: Chr05 Coordinates: 16000088-16006566 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6438 bp · LXL04_022971|LXL04_022971|OH1004|cDNA

atggattcatacgctttacgacaacaagaactcgactccgtcatgggcacgatgacccgtattccacgattaacctgtgctgacgggttccctgagtggaaatttcgcattgagagctacatcaaaggagctcatcctaaagtatggcgttgtatgatgcgtggtcctaacgtcatcaccgacACAGATACAGccactggtgctgtcaccatcaagcttcctgaaaactacaccgatgaggaatgggagaaagtggagga...

CDS

Download CDS FASTA

6438 bp · LXL04_022971|LXL04_022971|OH1004|CDS

ATGGATTCATACGCTTTACGACAACAAGAACTCGACTCCGTCATGGGCACGATGACCCGTATTCCACGATTAACCTGTGCTGACGGGTTCCCTGAGTGGAAATTTCGCATTGAGAGCTACATCAAAGGAGCTCATCCTAAAGTATGGCGTTGTATGATGCGTGGTCCTAACGTCATCACCGACACAGATACAGCCACTGGTGCTGTCACCATCAAGCTTCCTGAAAACTACACCGATGAGGAATGGGAGAAAGTGGAGGA...

Protein

Download Protein FASTA

2145 aa · LXL04_022971|LXL04_022971|OH1004|PROTEIN

MDSYALRQQELDSVMGTMTRIPRLTCADGFPEWKFRIESYIKGAHPKVWRCMMRGPNVITDTDTATGAVTIKLPENYTDEEWEKVEEDHKALGVLTMALTPDIAQGFREYTDAKALWKALSDVYEGNEDMKQSRQDLLRQKFNMFNHILGESLETQLQRFTTLTTELSTAGIVLTKSEINKKLLNSLPEKWDMNVLVIKKTSNLNTMTLAETLAVIKASEMDVKQREINRAGYSMGAPSNSAFAAQPSMAAPSPYGAPVA...

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_022971`
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_022971

Location Chr05:16000088-16006566 (-)

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: 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_022971 · 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.

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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.

Cytoplasm0.594

Rank 1 · LXL04_022971 · OH-1004

Nucleus0.433

Rank 2 · LXL04_022971 · OH-1004

Mitochondrion0.052

Rank 3 · LXL04_022971 · OH-1004

Endoplasmic reticulum0.051

Rank 4 · LXL04_022971 · OH-1004

Cell membrane0.047

Rank 5 · LXL04_022971 · 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.

PF14223.15Retrotran_gag_270-226 aa

PF00098.29zf-CCHC358-374 aa

PF00098.29zf-CCHC792-808 aa

PF22936.2Pol_BBD972-1046 aa

PF13976.12gag_pre-integrs1081-1151 aa

PF00665.33rve1169-1266 aa

PF29688.1TnsB_C1224-1282 aa

PF25597.2SH3_retrovirus1348-1396 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022971	`PF14223.15`	Retrotran_gag_2	70	226	3.9e-19	69.8
LXL04_022971	`PF00098.29`	zf-CCHC	358	374	3.2e-10	40.3
LXL04_022971	`PF00098.29`	zf-CCHC	792	808	3.2e-10	40.3
LXL04_022971	`PF22936.2`	Pol_BBD	972	1046	1.8e-15	57.8
LXL04_022971	`PF13976.12`	gag_pre-integrs	1081	1151	8.2e-17	61.5
LXL04_022971	`PF00665.33`	rve	1169	1266	2.9e-14	53.9
LXL04_022971	`PF29688.1`	TnsB_C	1224	1282	8.6e-06	26.3
LXL04_022971	`PF25597.2`	SH3_retrovirus	1348	1396	3e-12	46.9
LXL04_022971	`PF07727.20`	RVT_2	1665	1907	3.6e-75	253.4

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	35.009%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	35.363%	Swiss-Prot	weak database homology
`P92519`	Arabidopsis thaliana	Uncharacterized mitochondrial protein AtMg00810	36.486%	Swiss-Prot	weak database homology

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