TkA06G413950 | RubberDandelionOmics

Gene overview

TkA06G413950

Reference: TK1151 Chr: Chr06 Coordinates: 102450469-102455940 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2041 bp · TkA06G413950|TK1151|cDNA

TCTCAAATCTGCCACTGAAAGACAACTGATGCTGCCCGCTTACCACCGCTACTCCGCCTCCGCTGCACTGCACCACCGGAAAAGGATGGAGCGGGAACCCGGTATGTGGGAAGAGGTACCATTTCATAATAAAGGGTGATGGGGCTTCCATTGGTGGTTACAACAAATCATGTCTTGGTTGTGGAGCTTCCCTCCATTTATCCGACTCAAGGTGCAAGACATGCAACCATGTGATAACTACCGAAGACATTGAGGACCGG...

CDS

Download CDS FASTA

2007 bp · TkA06G413950|TK1151|CDS

ATGGTCGTCAACGGCCGTCCCTTGAAGAGGATGAAGAGGAGAGTAACCGCCGACCTCAACGATTTTCTAACTTTCCCCTCCGGCGATTTGACCCCGACGGCCCCTTTCAGGACTAGCGTCAGGGAGTTTTTGCTACGGCACGCGCTTCTTCCACCGCCTTCCTCCCTCCTACCACATCTGCTGACGTGGCAGATCCCGTTCCGGATTGGGGAACAGACCGTAGGCGGTGATGGTGATTCGTCCGTTTGCCTTGATGTGGT...

Protein

Download Protein FASTA

668 aa · TkA06G413950|TK1151|PROTEIN

MVVNGRPLKRMKRRVTADLNDFLTFPSGDLTPTAPFRTSVREFLLRHALLPPPSSLLPHLLTWQIPFRIGEQTVGGDGDSSVCLDVVEEDVIRSRSVYCDQCRVVGWSGNPVCGKRYHFIIKGDGASIGGYNKSCLGCGASLHLSDSRCKTCNHVITTEDIEDRMYNQLEDTNHLLHGVVHVNGYGHLLRVNGREGGSRVLSGSHIMDFWDRLCKLLGVRQVSVMDVSKKYDLDFRLLHSVVKGHPWYGNWGYKFGAGSY...

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	`TkA06G413950`
TK1151 ID	TkA06G413950
OH-1004 ID	LXL04_023022
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	82.400
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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	TK1151 / GWHBCHF00000000

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA06G413950

Location Chr06:102450469-102455940 (+)

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
`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
`At5g22260`	Transcriptional activator required for anther and post-meiotic pollen development and maturation.	No verified direct reference in this release
`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

View annotation sources

Functional annotation source: OH1004 · LXL04_023022 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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:AT5G22260

dosa:Os09g0449000

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

Open Annotation Module

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.

Nucleus0.951

Rank 1 · TkA06G413950 · TK1151

Cytoplasm0.097

Rank 2 · TkA06G413950 · TK1151

Cell membrane0.029

Rank 3 · TkA06G413950 · TK1151

Endoplasmic reticulum0.022

Rank 4 · TkA06G413950 · TK1151

Plastid0.013

Rank 5 · TkA06G413950 · TK1151

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.

PF20826PHD_580-93 aa

PF30977Bucky_ball89-171 aa

PF00628PHD93-103 aa

PF00628PHD135-144 aa

PF25874WHD_plant_repro152-169 aa

PF27744MS1_N175-181 aa

PF27744MS1_N234-275 aa

PF23202PAH_ZNF598280-329 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G413950	`PF20826`	PHD_5	80	93	0.0022	18.7
TkA06G413950	`PF30977`	Bucky_ball	89	171	0.38	10.0
TkA06G413950	`PF00628`	PHD	93	103	1.7e-06	28.7
TkA06G413950	`PF00628`	PHD	135	144	1.7e-06	28.7
TkA06G413950	`PF25874`	WHD_plant_repro	152	169	1e-10	42.1
TkA06G413950	`PF27744`	MS1_N	175	181	1.2e-20	74.0
TkA06G413950	`PF27744`	MS1_N	234	275	1.2e-20	74.0
TkA06G413950	`PF23202`	PAH_ZNF598	280	329	0.018	16.0
TkA06G413950	`PF27748`	MS1_C	290	320	6.3e-05	23.0
TkA06G413950	`PF25874`	WHD_plant_repro	351	428	1e-10	42.1
TkA06G413950	`PF25565`	Ubiquitin_At1g33420	501	590	5.7e-27	94.2
TkA06G413950	`PF00628`	PHD	612	656	1.7e-06	28.7
TkA06G413950	`PF20826`	PHD_5	612	656	0.0022	18.7
TkA06G413950	`PF31197`	PHD_JHD1	614	642	0.076	13.6

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
`Q9C810`	Arabidopsis thaliana	sp\|Q9C810\|Y1342_ARATH PHD finger protein At1g33420	50.400%	Swiss-Prot	High
`Q7X6Y7`	Arabidopsis thaliana	sp\|Q7X6Y7\|MMD1_ARATH PHD finger protein MALE MEIOCYTE DEATH 1	30.900%	Swiss-Prot	Medium
`Q9FMS5`	Arabidopsis thaliana	sp\|Q9FMS5\|MS1_ARATH PHD finger protein MALE STERILITY 1	31.500%	Swiss-Prot	Medium
`Q9ZUA9`	Arabidopsis thaliana	sp\|Q9ZUA9\|Y2181_ARATH PHD finger protein At2g01810	27.500%	Swiss-Prot	Low
`Q67V61`	Oryza sativa subsp. japonica	sp\|Q67V61\|PTC1_ORYSJ PHD finger protein PERSISTENT TAPETAL CELL 1	33.900%	Swiss-Prot	Medium

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