TkA03G460550 | RubberDandelionOmics

Gene overview

TkA03G460550

Reference: TK1151 Chr: Chr03 Coordinates: 114933413-114935358 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1179 bp · TkA03G460550|TK1151|cDNA

ATATTCCTATATCTAACCATTGCAGTTTGCCGCCATCTGATTTCTACTTCCAAACCTACGCGGGAACACAATCTAGAGTGAGAGGGAAAGAAAAGAATGAGGACGGAGGAAGACGAGGGCGCCGGCGAAGACATCCAAGTGGAGGAGGAGTTCAGTATATGGAAGAAGAACTCTCCGTTCTTATATGATCTCATCGTCTCCCACTCCCTTGAGTGGCCGTCGCTAACCGTTCATTGGCTCCCGTCACCACCAACTCCGTA...

CDS

Download CDS FASTA

1206 bp · TkA03G460550|TK1151|CDS

ATGAGGACGGAGGAAGACGAGGGCGCCGGCGAAGACATCCAAGTGGAGGAGGAGTTCAGTATATGGAAGAAGAACTCTCCGTTCTTATATGATCTCATCGTCTCCCACTCCCTTGAGTGGCCGTCGCTAACCGTTCATTGGCTCCCGTCACCACCAACTCCGTACAAAGACGGATCTTTCGCCACTCACAAGTTGATTCTCGGCACTCATACCTCCGATGAAAGCCCTAACTTTCTTCTCGTCGCAGATGTCCTCTTGCC...

Protein

Download Protein FASTA

401 aa · TkA03G460550|TK1151|PROTEIN

MRTEEDEGAGEDIQVEEEFSIWKKNSPFLYDLIVSHSLEWPSLTVHWLPSPPTPYKDGSFATHKLILGTHTSDESPNFLLVADVLLPVNPSSSLDTNHENPHTPKVDIVQKIHVDGEVNRARCMPQNPSIIAAKTSSSEVYVFDSTKQLLNDEGGSCEPDARLRGHEKEGYGLSWSPFKEGYLLSGSNDCKICLWDVSAMPSDKVLDAQHIYQDHGSLVEDVSWHLKNENLFGSVGDDCKLMIWDLRTNKHEQSVVVHEK...

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	`TkA03G460550`
TK1151 ID	TkA03G460550
OH-1004 ID	LXL04_009658
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 95.249 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

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA03G460550

Location Chr03:114933413-114935358 (+)

Description Similar to MSI3: WD-40 repeat-containing protein MSI3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g35050`	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA.	No verified direct reference in this release
`At2g16780`	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA.	No verified direct reference in this release
`At5g58230`	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA.	Arabidopsis MSI1 is required for epigenetic maintenance of reproductive development.2003 · DOI: 10.1242/dev.00470 Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development.2003 · DOI: 10.1093/emboj/cdg444 Identification of new members of Fertilisation Independent Seed Polycomb Group pathway involved in the control of seed development in Arabidopsis thaliana.2004 · DOI: 10.1242/dev.01168 Loss of function of MULTICOPY SUPPRESSOR OF IRA 1 produces nonviable parthenogenetic embryos in Arabidopsis.2005 · DOI: 10.1016/j.cub.2005.02.066 Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development.2006 · DOI: 10.1242/dev.02599 Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis.2008 · DOI: 10.1371/journal.pbio.0060194

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0640100`	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009658 · 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:0006260 DNA replication Biological Process

GO:0006281 DNA repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009555 pollen development Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009908 flower development Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010026 trichome differentiation Biological Process

GO:0010214 seed coat development Biological Process

KEGG gene cross-reference

ath:AT2G16780

ath:AT4G35050

ath:AT5G58230

dosa:Os03g0640100

sly:543534

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.

Nucleus0.828

Rank 1 · TkA03G460550 · TK1151

Cytoplasm0.340

Rank 2 · TkA03G460550 · TK1151

Cell membrane0.022

Rank 3 · TkA03G460550 · TK1151

Mitochondrion0.022

Rank 4 · TkA03G460550 · TK1151

Lysosome / Vacuole0.018

Rank 5 · TkA03G460550 · 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.

PF12265CAF1C_H4-bd17-87 aa

PF29037DSE1_N94-199 aa

PF23609Beta-prop_EIPR1105-195 aa

PF25171Beta-prop_WDR36-Utp21_1st107-133 aa

PF23775Beta-prop_RIG_2nd110-205 aa

PF24796WDR55110-338 aa

PF24807WD40_CDC20-Fz114-244 aa

PF23798Beta-prop_SPT8114-142 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G460550	`PF12265`	CAF1C_H4-bd	17	87	3.7e-26	91.9
TkA03G460550	`PF29037`	DSE1_N	94	199	7.5e-12	45.7
TkA03G460550	`PF23609`	Beta-prop_EIPR1	105	195	3.5e-17	63.5
TkA03G460550	`PF25171`	Beta-prop_WDR36-Utp21_1st	107	133	1.2e-10	42.0
TkA03G460550	`PF23775`	Beta-prop_RIG_2nd	110	205	5.2e-18	66.2
TkA03G460550	`PF24796`	WDR55	110	338	9.3e-12	45.3
TkA03G460550	`PF24807`	WD40_CDC20-Fz	114	244	2e-28	100.2
TkA03G460550	`PF23798`	Beta-prop_SPT8	114	142	0.034	13.7
TkA03G460550	`PF25173`	Beta-prop_WDR3_1st	116	288	6.3e-35	121.2
TkA03G460550	`PF24814`	WD40_Prp19	117	293	2.1e-20	73.7
TkA03G460550	`PF23098`	Beta-prop_NOL10_N	118	144	3.5e-05	23.8
TkA03G460550	`PF23756`	Beta-prop_HPS5	120	260	1.1e-06	28.9
TkA03G460550	`PF24817`	WD40_WDHD1_1st	130	148	1.6e-12	48.0
TkA03G460550	`PF25174`	Beta-prop_THOC3	135	200	9.5e-34	117.4
TkA03G460550	`PF24805`	EIF3I	136	225	6.4e-09	36.1
TkA03G460550	`PF25047`	Beta-prop_TEP1_2nd	137	262	3.3e-12	46.8

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
`O22469`	Arabidopsis thaliana	sp\|O22469\|MSI3_ARATH WD-40 repeat-containing protein MSI3	68.500%	Swiss-Prot	High
`O22468`	Arabidopsis thaliana	sp\|O22468\|MSI2_ARATH WD-40 repeat-containing protein MSI2	67.200%	Swiss-Prot	High
`O22467`	Arabidopsis thaliana	sp\|O22467\|MSI1_ARATH Histone-binding protein MSI1	57.200%	Swiss-Prot	High
`Q10G81`	Oryza sativa subsp. japonica	sp\|Q10G81\|MSI1_ORYSJ Histone-binding protein MSI1	55.800%	Swiss-Prot	High

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