LXL04_023019 | RubberDandelionOmics

Gene overview

LXL04_023019

Reference: OH-1004 Chr: Chr05 Coordinates: 19075471-19088009 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4227 bp · LXL04_023019|LXL04_023019|OH1004|cDNA

atgatgacacgaggacgtgctcatccactgactgtggaggagccgactgtttccatgactgtgtcaggcacgtattggccaatggttaccgcGGTTACGGTTAATcacatgatttatgtcaccgatatttatcaggggtctcgtgacactgttagaaaggattgggcagagatgttgttgccattattccgcgttgttacatatgttctgtattcgtacccttcttttcgtatcagcggtcagattcggaagtaccttca...

CDS

Download CDS FASTA

4227 bp · LXL04_023019|LXL04_023019|OH1004|CDS

ATGATGACACGAGGACGTGCTCATCCACTGACTGTGGAGGAGCCGACTGTTTCCATGACTGTGTCAGGCACGTATTGGCCAATGGTTACCGCGGTTACGGTTAATCACATGATTTATGTCACCGATATTTATCAGGGGTCTCGTGACACTGTTAGAAAGGATTGGGCAGAGATGTTGTTGCCATTATTCCGCGTTGTTACATATGTTCTGTATTCGTACCCTTCTTTTCGTATCAGCGGTCAGATTCGGAAGTACCTTCA...

Protein

Download Protein FASTA

1408 aa · LXL04_023019|LXL04_023019|OH1004|PROTEIN

MMTRGRAHPLTVEEPTVSMTVSGTYWPMVTAVTVNHMIYVTDIYQGSRDTVRKDWAEMLLPLFRVVTYVLYSYPSFRISGQIRKYLQESEGGLSSYAANTFGSGTFSFPPADLRSAIDIRRSSSCAAAATDELHVGNSSPPAYSSGDYQGLLQLTSSSLPRTVPASFPVSGEFPAIFCFRQFSDRPCCLSGEQHLVAGGFETSDKSLRVEASAQPTPSCRLSFSSRDVVTLWLLLTFHSSFQIKPGTISRGSRIHFTRIA...

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_023019`
TK1151 ID	TkAUNG036560
OH-1004 ID	LXL04_023019
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	67.700
Protein coverage (%)	TK1151 31.833 / OH-1004 5.824 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_023019

Location Chr05:19075471-19088009 (-)

Description Similar to Retrovirus-related Pol polyprotein from transposon TNT 1-94

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g02960`	Retrovirus-related Pol polyprotein from transposon RE2.	No verified direct reference in this release
`UniProt: Q94HW2`	Retrovirus-related Pol polyprotein from transposon RE1.	No verified direct reference in this release
`At3g18520`	Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).	PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings.2013 · DOI: 10.1105/tpc.113.109710 MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis.2019 · DOI: 10.1038/s41467-019-09417-1 HY5 Interacts with the Histone Deacetylase HDA15 to Repress Hypocotyl Cell Elongation in Photomorphogenesis.2019 · DOI: 10.1104/pp.19.00055 Arabidopsis histone deacetylase HDA15 directly represses plant response to elevated ambient temperature.2019 · DOI: 10.1111/tpj.14492

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_023019 · 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.

Cytoplasm0.432

Rank 1 · LXL04_023019 · OH-1004

Nucleus0.389

Rank 2 · LXL04_023019 · OH-1004

Endoplasmic reticulum0.097

Rank 3 · LXL04_023019 · OH-1004

Cell membrane0.094

Rank 4 · LXL04_023019 · OH-1004

Mitochondrion0.093

Rank 5 · LXL04_023019 · 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.

PF00850.25Hist_deacetyl468-540 aa

PF13976.12gag_pre-integrs884-926 aa

PF00665.33rve943-1040 aa

PF29688.1TnsB_C1005-1055 aa

PF07727.20RVT_21165-1304 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_023019	`PF00850.25`	Hist_deacetyl	468	540	1e-15	58.6
LXL04_023019	`PF13976.12`	gag_pre-integrs	884	926	3.5e-07	30.6
LXL04_023019	`PF00665.33`	rve	943	1040	2.8e-16	60.3
LXL04_023019	`PF29688.1`	TnsB_C	1005	1055	4.6e-08	33.7
LXL04_023019	`PF07727.20`	RVT_2	1165	1304	4.6e-32	112.3

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
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	46.358%	Swiss-Prot	weak database homology
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	44.371%	Swiss-Prot	weak database homology
`Q8GXJ1`	Arabidopsis thaliana	Histone deacetylase 15	41.935%	Swiss-Prot	weak database homology

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