LXL04_024288 | RubberDandelionOmics

Gene overview

LXL04_024288

Reference: OH-1004 Chr: Chr05 Coordinates: 86438985-86451914 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4218 bp · LXL04_024288|LXL04_024288|OH1004|cDNA

ATGAGAAGCACCGGAGAAGATCAGAAGCATTTTGTTCTCGTGCACGGTGCATGCCATGGCGCTTGGTGCTGGTTCAAGGTCAAACCTCTTCTTGAGGCTGCCGGCCACCGTGTCTCCGCCTTTGATCTCTCAGCCTCCGGCACAAACACCAGAATGATACAAGATGTCTCTACAGTTGCCGATTACAGTATGCCGTTGCTGGAATTCATGGCCACCATTCCGCCGGAGGAGAAGGTGGTGCTTGTCGGACATAGTCTTGG...

CDS

Download CDS FASTA

4218 bp · LXL04_024288|LXL04_024288|OH1004|CDS

ATGAGAAGCACCGGAGAAGATCAGAAGCATTTTGTTCTCGTGCACGGTGCATGCCATGGCGCTTGGTGCTGGTTCAAGGTCAAACCTCTTCTTGAGGCTGCCGGCCACCGTGTCTCCGCCTTTGATCTCTCAGCCTCCGGCACAAACACCAGAATGATACAAGATGTCTCTACAGTTGCCGATTACAGTATGCCGTTGCTGGAATTCATGGCCACCATTCCGCCGGAGGAGAAGGTGGTGCTTGTCGGACATAGTCTTGG...

Protein

Download Protein FASTA

1405 aa · LXL04_024288|LXL04_024288|OH1004|PROTEIN

MRSTGEDQKHFVLVHGACHGAWCWFKVKPLLEAAGHRVSAFDLSASGTNTRMIQDVSTVADYSMPLLEFMATIPPEEKVVLVGHSLGGLNLALAMEKFPEKVSVAVFVSAFMPDSVHTSSYVLDQYNERTPTEAWLDTQFLPYNTDESESSMFFGPKFLLEKLYQLCSEEDLELGKILIRPGSLFLKDLSKGKQFTEGRYGSVTRVFVICKEDRAIKEDFQRWMIGNNPVAEVKELNGVDHMPMLCDPNQLSSEFRSPKR...

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_024288`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_024288

Location Chr05:86438985-86451914 (-)

Description Similar to RE1: Retrovirus-related Pol polyprotein from transposon RE1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At2g23620`	Methylesterase shown to have carboxylesterase activity, methyl indole-3-acetic acid (MeIAA) esterase activity, methyl salicylate (MeSA) esterase activity and methyl jasmonate (MeJA) esterase activity in vitro.	Identification of likely orthologs of tobacco salicylic acid-binding protein 2 and their role in systemic acquired resistance in Arabidopsis thaliana.2008 · DOI: 10.1111/j.1365-313x.2008.03618.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024288 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006310 DNA recombination Biological Process

GO:0006508 proteolysis Biological Process

GO:0009694 jasmonic acid metabolic process Biological Process

GO:0009696 salicylic acid metabolic process Biological Process

GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway Biological Process

GO:0015074 DNA integration Biological Process

GO:0045087 innate immune response 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

nta:107791137

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.

Cytoplasm0.554

Rank 1 · LXL04_024288 · OH-1004

Nucleus0.390

Rank 2 · LXL04_024288 · OH-1004

Mitochondrion0.080

Rank 3 · LXL04_024288 · OH-1004

Peroxisome0.043

Rank 4 · LXL04_024288 · OH-1004

Cell membrane0.038

Rank 5 · LXL04_024288 · 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.

PF12146.16Hydrolase_48-112 aa

PF00561.27Abhydrolase_110-128 aa

PF12697.14Abhydrolase_611-245 aa

PF14223.15Retrotran_gag_2284-465 aa

PF22936.2Pol_BBD550-596 aa

PF13976.12gag_pre-integrs638-698 aa

PF29688.1TnsB_C727-801 aa

PF07727.20RVT_2967-1211 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024288	`PF12146.16`	Hydrolase_4	8	112	3.1e-08	33.9
LXL04_024288	`PF00561.27`	Abhydrolase_1	10	128	9.9e-17	62.1
LXL04_024288	`PF12697.14`	Abhydrolase_6	11	245	9.7e-22	79.4
LXL04_024288	`PF14223.15`	Retrotran_gag_2	284	465	1.8e-19	70.8
LXL04_024288	`PF22936.2`	Pol_BBD	550	596	3.5e-12	47.2
LXL04_024288	`PF13976.12`	gag_pre-integrs	638	698	7e-12	45.7
LXL04_024288	`PF29688.1`	TnsB_C	727	801	4.7e-08	33.7
LXL04_024288	`PF07727.20`	RVT_2	967	1211	5.6e-89	298.6

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	42.266%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	40.959%	Swiss-Prot	weak database homology
`Q8S8S9`	Arabidopsis thaliana	Methylesterase 1	61.847%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card