LXL04_033125 | RubberDandelionOmics

Gene overview

LXL04_033125

Reference: OH-1004 Chr: Chr07 Coordinates: 36736364-36744028 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2133 bp · LXL04_033125|LXL04_033125|OH1004|cDNA

ATGGTCGTCAACGGCCGTCCCTTAAAGAGGATGAAGAGGAGAGTAACCGCCGATCTCAACGATTTTCTTACTTTCCCCTCCGGCGATTTGACGCCAACGGCCCCTTTCAGGACCAGCGTGAGGGAGTTTTTGCTACGGCACGCCCTTCTTCCACCGCCTTCCTCTCTCCTACCACATCTGCTGACGTGGCAGATCCTCTTCCGGGTTGGGGAACAGACCGTAGCCGGTGATGGTGACGCGTCTGTTTGCCTTGATGTGGT...

CDS

Download CDS FASTA

2133 bp · LXL04_033125|LXL04_033125|OH1004|CDS

ATGGTCGTCAACGGCCGTCCCTTAAAGAGGATGAAGAGGAGAGTAACCGCCGATCTCAACGATTTTCTTACTTTCCCCTCCGGCGATTTGACGCCAACGGCCCCTTTCAGGACCAGCGTGAGGGAGTTTTTGCTACGGCACGCCCTTCTTCCACCGCCTTCCTCTCTCCTACCACATCTGCTGACGTGGCAGATCCTCTTCCGGGTTGGGGAACAGACCGTAGCCGGTGATGGTGACGCGTCTGTTTGCCTTGATGTGGT...

Protein

Download Protein FASTA

710 aa · LXL04_033125|LXL04_033125|OH1004|PROTEIN

MVVNGRPLKRMKRRVTADLNDFLTFPSGDLTPTAPFRTSVREFLLRHALLPPPSSLLPHLLTWQILFRVGEQTVAGDGDASVCLDVVEEDVIRSRSVYCDQCRVVGWSGNPVCGKRYHFIIKGDGASIGGYNKSCPSCGASLHLSDSRCKTCSHVMTTEDVEDWMYNQLEDTNHLLHGVVHVNGYGHLLRVNGREGGSRVLSGTHIMDFWDRLCKLLGVRQVSVMDVSKKYGLDFRLLHSVVKGHPWYGDWGYNFGAGSY...

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_033125`
TK1151 ID	TkA08G233450
OH-1004 ID	LXL04_033125
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 98.944 / OH-1004 92.394 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_033125

Location Chr07:36736364-36744028 (-)

Description Similar to At1g33420: PHD finger protein At1g33420

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g33420`	PHD finger protein At1g33420.	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
`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

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

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Functional annotation source: OH1004 · LXL04_033125 · 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.

Nucleus0.942

Rank 1 · LXL04_033125 · OH-1004

Cytoplasm0.114

Rank 2 · LXL04_033125 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_033125 · OH-1004

Endoplasmic reticulum0.024

Rank 4 · LXL04_033125 · OH-1004

Mitochondrion0.012

Rank 5 · LXL04_033125 · 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.

PF27744.1MS1_N234-276 aa

PF27748.1MS1_C284-319 aa

PF25874.1WHD_plant_repro349-427 aa

PF25565.2Ubiquitin_At1g33420485-564 aa

PF00628.36PHD605-649 aa

PF00628.36PHD660-696 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_033125	`PF27744.1`	MS1_N	234	276	2.3e-20	73.0
LXL04_033125	`PF27748.1`	MS1_C	284	319	7.1e-07	29.3
LXL04_033125	`PF25874.1`	WHD_plant_repro	349	427	9.1e-11	42.2
LXL04_033125	`PF25565.2`	Ubiquitin_At1g33420	485	564	1.1e-23	83.7
LXL04_033125	`PF00628.36`	PHD	605	649	2.2e-11	44.3
LXL04_033125	`PF00628.36`	PHD	660	696	2.2e-11	44.3

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
`Q9C810`	Arabidopsis thaliana	PHD finger protein At1g33420	49.335%	Swiss-Prot	moderate database homology
`Q9FMS5`	Arabidopsis thaliana	PHD finger protein MALE STERILITY 1	31.579%	Swiss-Prot	moderate database homology
`Q7X6Y7`	Arabidopsis thaliana	PHD finger protein MALE MEIOCYTE DEATH 1	30.964%	Swiss-Prot	moderate database homology
`Q9ZUA9`	Arabidopsis thaliana	PHD finger protein At2g01810	27.815%	Swiss-Prot	weak database homology
`Q67V61`	Oryza sativa subsp. japonica	PHD finger protein PERSISTENT TAPETAL CELL 1	34.138%	Swiss-Prot	moderate database homology

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