LXL04_012621 | RubberDandelionOmics

Gene overview

LXL04_012621

Reference: OH-1004 Chr: Chr03 Coordinates: 15748013-15755289 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4122 bp · LXL04_012621|LXL04_012621|OH1004|cDNA

ATGAAAGCCATTGACATACTTTGTGCTTCCCAAGCTGCAACCTCCATCGTAGACTACATGGATTCTAATCAACAAccatcctcctcctcctcctcctcctcctccaccgGTGGCAGAGCAATCGACCGCCACAACCCCATTATCCAAGATCAAAAAAGACTTACCAGAAATACCCTTCTCCCTTCCTCCATCACTCCaaacaaaaacaagaagaatccAAAAAACAGCGACCAGAAAAGAAAAACAATTGCTTTTGCCGA...

CDS

Download CDS FASTA

4122 bp · LXL04_012621|LXL04_012621|OH1004|CDS

ATGAAAGCCATTGACATACTTTGTGCTTCCCAAGCTGCAACCTCCATCGTAGACTACATGGATTCTAATCAACAACCATCCTCCTCCTCCTCCTCCTCCTCCTCCACCGGTGGCAGAGCAATCGACCGCCACAACCCCATTATCCAAGATCAAAAAAGACTTACCAGAAATACCCTTCTCCCTTCCTCCATCACTCCAAACAAAAACAAGAAGAATCCAAAAAACAGCGACCAGAAAAGAAAAACAATTGCTTTTGCCGA...

Protein

Download Protein FASTA

1373 aa · LXL04_012621|LXL04_012621|OH1004|PROTEIN

MKAIDILCASQAATSIVDYMDSNQQPSSSSSSSSSTGGRAIDRHNPIIQDQKRLTRNTLLPSSITPNKNKKNPKNSDQKRKTIAFADENSDQQLITNKNNSVKNPSSSATTVVRRQGGALLGWGCTRPGDFISPATSSRFLLADKALSDQYDPLLKQVSPPPLPAPEKPDKVENDDSVEKKDDGHLPSSPPKTTPRSSSSLSSRSSNQQVVVLRVSLHCKGCEKKMRKHISKMEGVKDFTIDFMAKKVTVIGDVTPLAVL...

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_012621`
TK1151 ID	TkA02G549240
OH-1004 ID	LXL04_012621
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	97.700
Protein coverage (%)	TK1151 99.338 / OH-1004 21.704 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_012621

Location Chr03:15748013-15755289 (-)

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
`At2g37390`	Protein SODIUM POTASSIUM ROOT DEFECTIVE 2.	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_012621 · 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.

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.

Cytoplasm0.563

Rank 1 · LXL04_012621 · OH-1004

Nucleus0.518

Rank 2 · LXL04_012621 · OH-1004

Mitochondrion0.070

Rank 3 · LXL04_012621 · OH-1004

Endoplasmic reticulum0.027

Rank 4 · LXL04_012621 · OH-1004

Plastid0.026

Rank 5 · LXL04_012621 · 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.

PF00403.33HMA213-258 aa

PF14223.15Retrotran_gag_2346-518 aa

PF22936.2Pol_BBD608-686 aa

PF13976.12gag_pre-integrs718-784 aa

PF00665.33rve798-895 aa

PF25597.2SH3_retrovirus969-1030 aa

PF07727.20RVT_21217-1275 aa

PF07727.20RVT_21277-1351 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012621	`PF00403.33`	HMA	213	258	1.4e-10	42.1
LXL04_012621	`PF14223.15`	Retrotran_gag_2	346	518	2.9e-20	73.4
LXL04_012621	`PF22936.2`	Pol_BBD	608	686	9e-15	55.5
LXL04_012621	`PF13976.12`	gag_pre-integrs	718	784	1.2e-08	35.4
LXL04_012621	`PF00665.33`	rve	798	895	1.4e-08	35.6
LXL04_012621	`PF25597.2`	SH3_retrovirus	969	1030	7.9e-21	74.3
LXL04_012621	`PF07727.20`	RVT_2	1217	1275	7.3e-37	128.0
LXL04_012621	`PF07727.20`	RVT_2	1277	1351	7.3e-37	128.0

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	39.263%	Swiss-Prot	moderate database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	37.381%	Swiss-Prot	moderate database homology
`Q58FZ0`	Arabidopsis thaliana	Protein SODIUM POTASSIUM ROOT DEFECTIVE 2	36.111%	Swiss-Prot	weak database homology

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