LXL04_014884 | RubberDandelionOmics

Gene overview

LXL04_014884

Reference: OH-1004 Chr: Chr03 Coordinates: 58915246-58930624 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5580 bp · LXL04_014884|LXL04_014884|OH1004|cDNA

ATGGGGAGGATTTCGGCTGTCGAAATTACTTTACAATCGTTTACCAGTGGAGATGACATCATTCGGAAAATTATCGAGATCTGGGGCCAATTTAGAGTGCCAATTTTAGCGCCATTGTTAAGAATCTTGATGTATGTTTCTCTTGCGATGTCCATAATGTTGTTCTTAGAGAAGGTTTATATGTCATTGGTGGTTGGATTCAATTGGTTATTTCTAAGAAAGACAGAAAAACGCTACAAATGGGAAGAATTCAAAAAAGA...

CDS

Download CDS FASTA

5580 bp · LXL04_014884|LXL04_014884|OH1004|CDS

ATGGGGAGGATTTCGGCTGTCGAAATTACTTTACAATCGTTTACCAGTGGAGATGACATCATTCGGAAAATTATCGAGATCTGGGGCCAATTTAGAGTGCCAATTTTAGCGCCATTGTTAAGAATCTTGATGTATGTTTCTCTTGCGATGTCCATAATGTTGTTCTTAGAGAAGGTTTATATGTCATTGGTGGTTGGATTCAATTGGTTATTTCTAAGAAAGACAGAAAAACGCTACAAATGGGAAGAATTCAAAAAAGA...

Protein

Download Protein FASTA

1859 aa · LXL04_014884|LXL04_014884|OH1004|PROTEIN

MGRISAVEITLQSFTSGDDIIRKIIEIWGQFRVPILAPLLRILMYVSLAMSIMLFLEKVYMSLVVGFNWLFLRKTEKRYKWEEFKKDVESGNSVYPLVLIQIPMFNEREVYQLSIGAACALSWPSDRIVIQVLDDSTDPIIKDMVEVECQKWASKGTNIHYQVRDNRKGYKAGALKEGLKHPYANECEYVAIFDADFQPEPDFLWKTIPFLYHNSTLGLVQTRWKFEQGSPQITPSSSPPPSPKTSTMSGESHNLATNLK...

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_014884`
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_014884

Location Chr03:58915246-58930624 (+)

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
`At5g03760`	Possesses glucomannan synthase and mannan synthase activities in vitro.	Agrobacterium-mediated root transformation is inhibited by mutation of an Arabidopsis cellulose synthase-like gene.2003 · DOI: 10.1104/pp.103.030726

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0625700`	Probable mannan synthase which consists of a 4-beta-mannosyltransferase activity on mannan using GDP-mannose.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_014884 · 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.

Cytoplasm0.492

Rank 1 · LXL04_014884 · OH-1004

Nucleus0.267

Rank 2 · LXL04_014884 · OH-1004

Mitochondrion0.119

Rank 3 · LXL04_014884 · OH-1004

Endoplasmic reticulum0.106

Rank 4 · LXL04_014884 · OH-1004

Peroxisome0.080

Rank 5 · LXL04_014884 · 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.

PF00535.33Glycos_transf_2102-239 aa

PF14223.15Retrotran_gag_2286-460 aa

PF13976.12gag_pre-integrs571-614 aa

PF00665.33rve627-725 aa

PF25597.2SH3_retrovirus799-860 aa

PF07727.20RVT_21009-1252 aa

PF13632.13Glyco_trans_2_31507-1690 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014884	`PF00535.33`	Glycos_transf_2	102	239	2.2e-10	41.4
LXL04_014884	`PF14223.15`	Retrotran_gag_2	286	460	2.9e-24	86.4
LXL04_014884	`PF13976.12`	gag_pre-integrs	571	614	7e-09	36.1
LXL04_014884	`PF00665.33`	rve	627	725	5.2e-08	33.8
LXL04_014884	`PF25597.2`	SH3_retrovirus	799	860	8.2e-23	80.7
LXL04_014884	`PF07727.20`	RVT_2	1009	1252	2.1e-69	234.5
LXL04_014884	`PF13632.13`	Glyco_trans_2_3	1507	1690	3.9e-11	43.9

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
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	55.114%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	52.773%	Swiss-Prot	weak database homology
`Q9LZR3`	Arabidopsis thaliana	Glucomannan 4-beta-mannosyltransferase 9	62.060%	Swiss-Prot	weak database homology
`Q67VS7`	Oryza sativa subsp. japonica	Probable glucomannan 4-beta-mannosyltransferase 9	53.717%	Swiss-Prot	weak database homology

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