LXL04_008822 | RubberDandelionOmics

Gene overview

LXL04_008822

Reference: OH-1004 Chr: Chr02 Coordinates: 109744573-109750028 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4899 bp · LXL04_008822|LXL04_008822|OH1004|cDNA

ATGGAATGTGATGATAACAAACCCGGATCAAGTGAAGGATTGCTTGAAACTGGGATAGGGTTTGATGCAAATTCTGCTGTTAGCAAAACTAGGGTTGAGAAGTCGGATATGGAAAATTTGGGGAAAAATAAGAGATCTTCCGAAATCAAATCTGGATTTGAGTCTGATGATGACGAGCCGATTGGTTCTATGTTTCAGATTAAAAACAGAAGGAACCCTAAGAAGGTTAAGGTTGAAAATGATGTGTCTGAAGATCTGGA...

CDS

Download CDS FASTA

4899 bp · LXL04_008822|LXL04_008822|OH1004|CDS

ATGGAATGTGATGATAACAAACCCGGATCAAGTGAAGGATTGCTTGAAACTGGGATAGGGTTTGATGCAAATTCTGCTGTTAGCAAAACTAGGGTTGAGAAGTCGGATATGGAAAATTTGGGGAAAAATAAGAGATCTTCCGAAATCAAATCTGGATTTGAGTCTGATGATGACGAGCCGATTGGTTCTATGTTTCAGATTAAAAACAGAAGGAACCCTAAGAAGGTTAAGGTTGAAAATGATGTGTCTGAAGATCTGGA...

Protein

Download Protein FASTA

1632 aa · LXL04_008822|LXL04_008822|OH1004|PROTEIN

MECDDNKPGSSEGLLETGIGFDANSAVSKTRVEKSDMENLGKNKRSSEIKSGFESDDDEPIGSMFQIKNRRNPKKVKVENDVSEDLELGGMNDTLATFRKKIKGPKVSRANATKGKDLNTDIKEPLNQSSIGAVNNADLASKSVPNTMTKQQIVSEDAIIVTKGSKNNSKEKIKRSKSKSTKKKGSGGTKSDENLTENCLDDHLEDSLSVLLQKARKNSKLKQLKSTEPHKDAVDQNPNDSVHEPNTIPALSVEKSQNDG...

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_008822`
TK1151 ID	TkA03G329140
OH-1004 ID	LXL04_008822
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	96.400
Protein coverage (%)	TK1151 100.000 / OH-1004 39.583 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_008822

Location Chr02:109744573-109750028 (+)

Description Similar to LDL3: Lysine-specific histone demethylase 1 homolog 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`UniProt: F4JLS1`	Probable histone demethylase that reduces the levels of histone H3 'Lys-4' methylation in chromatin.	No verified direct reference in this release
`At3g10390`	Probable histone demethylase that promotes flowering independently of the photoperiod and vernalization pathways by repressing FLOWERING LOCUS C (FLC), a floral repressor that blocks the transition from vegetative to reproductive development.	No verified direct reference in this release
`At1g62830`	Probable histone demethylase that reduces the levels of histone H3 'Lys-4' methylation in chromatin of the floral repressor FLOWERING LOCUS C (FLC) and the sporophytically silenced floral repressor FWA.	Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition.2007 · DOI: 10.1105/tpc.107.052373 Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone deubiquitinase complexes in plant gene repression.2011 · DOI: 10.1073/pnas.1014030108 Arabidopsis histone demethylases LDL1 and LDL2 control primary seed dormancy by regulating DELAY OF GERMINATION 1 and ABA signaling-related genes.2015 · DOI: 10.3389/fpls.2015.00159

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0755200`	Probable histone demethylase.	No verified direct reference in this release
`Os08g0143400`	Probable histone demethylase.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008822 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009627 systemic acquired resistance Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0046208 spermine catabolic process Biological Process

GO:0048364 root development Biological Process

GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process

GO:1903602 thermospermine catabolic process Biological Process

GO:1904629 response to diterpene Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G62830

ath:AT3G10390

ath:AT4G16310

dosa:Os02g0755200

dosa:Os08g0143400

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.844

Rank 1 · LXL04_008822 · OH-1004

Cytoplasm0.144

Rank 2 · LXL04_008822 · OH-1004

Cell membrane0.084

Rank 3 · LXL04_008822 · OH-1004

Endoplasmic reticulum0.051

Rank 4 · LXL04_008822 · OH-1004

Golgi apparatus0.021

Rank 5 · LXL04_008822 · 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.

PF04433.24SWIRM488-558 aa

PF07992.21Pyr_redox_2649-698 aa

PF01266.31DAO659-693 aa

PF03486.21HI0933_like659-696 aa

PF12831.14FAD_oxidored660-696 aa

PF13450.13NAD_binding_8662-718 aa

PF01593.31Amino_oxidase668-1110 aa

PF23030.2SCAF11-like_C1546-1597 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008822	`PF04433.24`	SWIRM	488	558	3.6e-15	56.7
LXL04_008822	`PF07992.21`	Pyr_redox_2	649	698	2.3e-10	41.1
LXL04_008822	`PF01266.31`	DAO	659	693	1.2e-06	29.1
LXL04_008822	`PF03486.21`	HI0933_like	659	696	2.1e-06	28.1
LXL04_008822	`PF12831.14`	FAD_oxidored	660	696	4.8e-06	26.8
LXL04_008822	`PF13450.13`	NAD_binding_8	662	718	4.7e-14	53.1
LXL04_008822	`PF01593.31`	Amino_oxidase	668	1110	6.2e-89	300.0
LXL04_008822	`PF23030.2`	SCAF11-like_C	1546	1597	2.8e-07	31.3

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
`F4JLS1`	Arabidopsis thaliana	Lysine-specific histone demethylase 1 homolog 3	53.532%	Swiss-Prot	strong database homology
`Q9CAE3`	Arabidopsis thaliana	Protein FLOWERING LOCUS D	40.481%	Swiss-Prot	weak database homology
`Q8VXV7`	Arabidopsis thaliana	Lysine-specific histone demethylase 1 homolog 1	39.871%	Swiss-Prot	weak database homology
`Q6Z690`	Oryza sativa subsp. japonica	Lysine-specific histone demethylase 1 homolog 1	39.911%	Swiss-Prot	weak database homology
`Q6YYZ1`	Oryza sativa subsp. japonica	Lysine-specific histone demethylase 1 homolog 2	39.002%	Swiss-Prot	weak database homology

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