LXL04_005311 | RubberDandelionOmics

Gene overview

LXL04_005311

Reference: OH-1004 Chr: Chr01 Coordinates: 160120804-160128336 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3798 bp · LXL04_005311|LXL04_005311|OH1004|cDNA

ATGAAAGAAGGTACGTATGACAGGGCTCGGAGCGCCGATAAGGTACCTTCGGCCCTGACCGCATTAAATACGATTGGAGTTACACCTACATTACCGAGTCTTTGTCAACGGCCCCTTTCTGCCTCTACTCATATCGCAGCCATCATGTCTACCATAGTTGAGGTTACTACCTATACACACTTCCCAATCAAACTCACAGCTCACAATTTCCCTGTCTGGCGAAAGCAAGTGCTCGCAACCCTAACAGGATTAGGGCTCGA...

CDS

Download CDS FASTA

3798 bp · LXL04_005311|LXL04_005311|OH1004|CDS

ATGAAAGAAGGTACGTATGACAGGGCTCGGAGCGCCGATAAGGTACCTTCGGCCCTGACCGCATTAAATACGATTGGAGTTACACCTACATTACCGAGTCTTTGTCAACGGCCCCTTTCTGCCTCTACTCATATCGCAGCCATCATGTCTACCATAGTTGAGGTTACTACCTATACACACTTCCCAATCAAACTCACAGCTCACAATTTCCCTGTCTGGCGAAAGCAAGTGCTCGCAACCCTAACAGGATTAGGGCTCGA...

Protein

Download Protein FASTA

1265 aa · LXL04_005311|LXL04_005311|OH1004|PROTEIN

MKEGTYDRARSADKVPSALTALNTIGVTPTLPSLCQRPLSASTHIAAIMSTIVEVTTYTHFPIKLTAHNFPVWRKQVLATLTGLGLDGYVTGSIVAPSKILSTDNTKSNPAYLPWFRQDQIILGALLGSCSETIQPIVSSTETAHEAFKRLTASYASVSRSRIISLKSRLANNPKGTRSITDFLLDMKNIADDISLAQSLVDEEDLIVHILGQLGEEYNHISSALKIRDTPITFPDLFDKLLDHERTLKDTQTPPAIATV...

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_005311`
TK1151 ID	TkA01G067440
OH-1004 ID	LXL04_005311
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	98.900
Protein coverage (%)	TK1151 93.426 / OH-1004 21.344 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_005311

Location Chr01:160120804-160128336 (+)

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

View annotation sources

Functional annotation source: OH1004 · LXL04_005311 · 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.

Cytoplasm0.675

Rank 1 · LXL04_005311 · OH-1004

Nucleus0.440

Rank 2 · LXL04_005311 · OH-1004

Mitochondrion0.083

Rank 3 · LXL04_005311 · OH-1004

Peroxisome0.030

Rank 4 · LXL04_005311 · OH-1004

Plastid0.025

Rank 5 · LXL04_005311 · 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.

PF14223.15Retrotran_gag_279-252 aa

PF00665.33rve347-445 aa

PF25597.2SH3_retrovirus519-581 aa

PF07727.20RVT_2729-823 aa

PF07727.20RVT_2824-940 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005311	`PF14223.15`	Retrotran_gag_2	79	252	2.3e-17	64.0
LXL04_005311	`PF00665.33`	rve	347	445	3.5e-12	47.2
LXL04_005311	`PF25597.2`	SH3_retrovirus	519	581	3.6e-18	65.8
LXL04_005311	`PF07727.20`	RVT_2	729	823	3.5e-48	165.1
LXL04_005311	`PF07727.20`	RVT_2	824	940	3.5e-48	165.1

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	51.479%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	50.791%	Swiss-Prot	weak database homology
`P92519`	Arabidopsis thaliana	Uncharacterized mitochondrial protein AtMg00810	48.246%	Swiss-Prot	weak database homology

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