LXL04_024846 | RubberDandelionOmics

Gene overview

LXL04_024846

Reference: OH-1004 Chr: Chr05 Coordinates: 100387675-100390136 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2043 bp · LXL04_024846|LXL04_024846|OH1004|cDNA

ATGTCGATTCCCATTATCAAGATGATCGGAGCTAGTAATACCAGCAAGAAGCGAAAGATGAAATCAGCAAAGTATTACGGATTACAGAGCTTTCTTCAACCTGGTTGCCCACTCTCGTTGTCTGGTTCGTTTAGAGACAATGTCAGGAGATTTATTCAAGAATGCGGTCAGCTTGAGGATTACAAAATTGAAGGAATGCCGATATGGTGCACCTTTCTCGTTCACGAACATCGGGGTTTTGTGCTTCCGTTGTATACTTT...

CDS

Download CDS FASTA

2043 bp · LXL04_024846|LXL04_024846|OH1004|CDS

ATGTCGATTCCCATTATCAAGATGATCGGAGCTAGTAATACCAGCAAGAAGCGAAAGATGAAATCAGCAAAGTATTACGGATTACAGAGCTTTCTTCAACCTGGTTGCCCACTCTCGTTGTCTGGTTCGTTTAGAGACAATGTCAGGAGATTTATTCAAGAATGCGGTCAGCTTGAGGATTACAAAATTGAAGGAATGCCGATATGGTGCACCTTTCTCGTTCACGAACATCGGGGTTTTGTGCTTCCGTTGTATACTTT...

Protein

Download Protein FASTA

680 aa · LXL04_024846|LXL04_024846|OH1004|PROTEIN

MSIPIIKMIGASNTSKKRKMKSAKYYGLQSFLQPGCPLSLSGSFRDNVRRFIQECGQLEDYKIEGMPIWCTFLVHEHRGFVLPLYTFEECVNNSLQPLCDHCRCSGWSHHFVSKRKYHFIIPIDNEWNKPTEDGVLDVQSHILHGLIHCNGFGHLLCINGIEGGSNFIYGREVMDLWDRICTTLHTRKISVVDNSKKRKMDLRLLYGVSYGHTWFGRWDYKFCHGSFGVTKDKYQQALQILSTLQLNIIVQDSQNCSVKK...

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_024846`
TK1151 ID	TkA06G102290
OH-1004 ID	LXL04_024846
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 48.235 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_024846

Location Chr05:100387675-100390136 (+)

Description Similar to MMD1: PHD finger protein MALE MEIOCYTE DEATH 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g66170`	Probable transcription factor required for chromosome organization and progression during male meiosis (e.g. microsporogenesis).	The Arabidopsis MALE MEIOCYTE DEATH1 gene encodes a PHD-finger protein that is required for male meiosis.2003 · DOI: 10.1105/tpc.010447 The DUET gene is necessary for chromosome organization and progression during male meiosis in Arabidopsis and encodes a PHD finger protein.2003 · DOI: 10.1242/dev.00827 The PHD Finger Protein MMD1/DUET Ensures the Progression of Male Meiotic Chromosome Condensation and Directly Regulates the Expression of the Condensin Gene CAP-D3.2016 · DOI: 10.1105/tpc.16.00040 Cell-type-dependent histone demethylase specificity promotes meiotic chromosome condensation in Arabidopsis.2020 · DOI: 10.1038/s41477-020-0697-0
`At2g01810`	PHD finger protein At2g01810.	No verified direct reference in this release
`At5g22260`	Transcriptional activator required for anther and post-meiotic pollen development and maturation.	No verified direct reference in this release
`At1g33420`	PHD finger protein At1g33420.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0449000`	Probable transcriptional activator required for tapetal programmed cell death (PCD) and degeneration, and pollen development in anthers.	PERSISTENT TAPETAL CELL1 encodes a PHD-finger protein that is required for tapetal cell death and pollen development in rice.2011 · DOI: 10.1104/pp.111.175760

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024846 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000212 meiotic spindle organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0007060 male meiosis chromosome segregation Biological Process

GO:0007140 male meiotic nuclear division Biological Process

GO:0009555 pollen development Biological Process

GO:0009846 pollen germination Biological Process

GO:0010032 meiotic chromosome condensation Biological Process

GO:0010208 pollen wall assembly Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0022414 reproductive process Biological Process

GO:0043068 positive regulation of programmed cell death Biological Process

KEGG gene cross-reference

ath:AT1G33420

ath:AT1G66170

ath:AT2G01810

ath:AT5G22260

dosa:Os09g0449000

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.

Nucleus0.932

Rank 1 · LXL04_024846 · OH-1004

Cytoplasm0.114

Rank 2 · LXL04_024846 · OH-1004

Cell membrane0.039

Rank 3 · LXL04_024846 · OH-1004

Endoplasmic reticulum0.023

Rank 4 · LXL04_024846 · OH-1004

Plastid0.018

Rank 5 · LXL04_024846 · 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.

PF27744.1MS1_N201-244 aa

PF27748.1MS1_C249-291 aa

PF25874.1WHD_plant_repro329-406 aa

PF25565.2Ubiquitin_At1g33420480-576 aa

PF20826.3PHD_5590-644 aa

PF00628.36PHD598-642 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024846	`PF27744.1`	MS1_N	201	244	2.4e-23	82.6
LXL04_024846	`PF27748.1`	MS1_C	249	291	5.6e-14	52.0
LXL04_024846	`PF25874.1`	WHD_plant_repro	329	406	7.5e-35	119.4
LXL04_024846	`PF25565.2`	Ubiquitin_At1g33420	480	576	5e-27	94.3
LXL04_024846	`PF20826.3`	PHD_5	590	644	8.2e-06	26.5
LXL04_024846	`PF00628.36`	PHD	598	642	5.9e-07	30.1

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q7X6Y7`	Arabidopsis thaliana	PHD finger protein MALE MEIOCYTE DEATH 1	47.668%	Swiss-Prot	moderate database homology
`Q9ZUA9`	Arabidopsis thaliana	PHD finger protein At2g01810	41.026%	Swiss-Prot	moderate database homology
`Q9FMS5`	Arabidopsis thaliana	PHD finger protein MALE STERILITY 1	32.471%	Swiss-Prot	moderate database homology
`Q9C810`	Arabidopsis thaliana	PHD finger protein At1g33420	31.803%	Swiss-Prot	moderate database homology
`Q67V61`	Oryza sativa subsp. japonica	PHD finger protein PERSISTENT TAPETAL CELL 1	32.479%	Swiss-Prot	moderate database homology

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