TkA04G458280 | RubberDandelionOmics

Gene overview

TkA04G458280

Reference: TK1151 Chr: Chr04 Coordinates: 115583854-115587767 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1378 bp · TkA04G458280|TK1151|cDNA

GCCATGGTCTTTTTTGGAGCGTTTTGAAAAGACTGATGGATTATTTTGGGGCGGTTCGTCACGCAATCCAAGTCTTTTTATGTCATTTGAATTTCAAAGAGACTCCGAAACCATACTCCATTGAGAGGGGAGATAGACTGCCGATCAAAGATGTATTAGATACGGTTCTTGCTACGATTGGTGATTAACGACGCGCCTGAGTGACTCTAGCGCACCGTGGAATGGTTCCCAGATCGTGACGAACATGCTAGAAACTACCA...

CDS

Download CDS FASTA

846 bp · TkA04G458280|TK1151|CDS

ATGCCTCAAAACTATTCTATTATTGCCACAAAGAGTGTCCATTCAGACGTTTTTGTTTTTGCTAGTGAGTTTCATCCAATTAAGCCTTTTCCTGATGAAAATGAAACATGCAATCCTGATTTGAGATTAAGGGGTCATGAAAATGATGGATTTGGGTTGTCATGGAGTAAGTTCAAAGAGGGTTGGCTATTGAGCGGGTCTTATGATGGAAAAATCTGCATGTGGGACATAAATGGGACCCCAGAGGATCAAGCTATGGA...

Protein

Download Protein FASTA

281 aa · TkA04G458280|TK1151|PROTEIN

MPQNYSIIATKSVHSDVFVFASEFHPIKPFPDENETCNPDLRLRGHENDGFGLSWSKFKEGWLLSGSYDGKICMWDINGTPEDQAMDAMQVYKVHNAPVEDVAWSLRHDYLFASCGYDKYVHIFDLRSPCFTRPIQSLMAHPSAINCLSFNPFNEWLLATGSTDKTMKLFDLRKFTSARHTFNHHMNEVVQVGWSPQDETILASSCSGRRLMVWDLSRIGQEQTSEDGEDGPPELMFIHGGHTSKVCDFSWNPCEDWVIA...

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	`TkA04G458280`
TK1151 ID	TkA04G458280
OH-1004 ID	LXL04_038714
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 65.654 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 TkA04G458280

Location Chr04:115583854-115587767 (-)

Description Similar to MSI1: WD-40 repeat-containing protein MSI1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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_038714 · 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:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0006260 DNA replication Biological Process

GO:0006281 DNA repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006335 DNA replication-dependent chromatin assembly 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:0007307 eggshell chorion gene amplification Biological Process

GO:0007346 regulation of mitotic cell cycle Biological Process

GO:0007379 segment specification Biological Process

KEGG gene cross-reference

ath:AT5G58230

ddi:DDB_G0282529

dme:Dmel_CG4236

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.

Nucleus0.698

Rank 1 · TkA04G458280 · TK1151

Cytoplasm0.379

Rank 2 · TkA04G458280 · TK1151

Mitochondrion0.035

Rank 3 · TkA04G458280 · TK1151

Cell membrane0.031

Rank 4 · TkA04G458280 · TK1151

Lysosome / Vacuole0.025

Rank 5 · TkA04G458280 · 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.

PF24807WD40_CDC20-Fz14-116 aa

PF25175Beta-prop_WDR518-78 aa

PF23869Beta-prop_WDR75_1st25-77 aa

PF23775Beta-prop_RIG_2nd32-82 aa

PF25173Beta-prop_WDR3_1st39-172 aa

PF24105Beta-prop_CAF1B_HIR141-128 aa

PF23381Beta-prop_IFT122_1st42-80 aa

PF24817WD40_WDHD1_1st42-124 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G458280	`PF24807`	WD40_CDC20-Fz	14	116	6.3e-37	128.2
TkA04G458280	`PF25175`	Beta-prop_WDR5	18	78	6e-28	98.7
TkA04G458280	`PF23869`	Beta-prop_WDR75_1st	25	77	4.4e-06	27.0
TkA04G458280	`PF23775`	Beta-prop_RIG_2nd	32	82	2.2e-18	67.4
TkA04G458280	`PF25173`	Beta-prop_WDR3_1st	39	172	8.7e-23	81.7
TkA04G458280	`PF24105`	Beta-prop_CAF1B_HIR1	41	128	1.4e-18	67.8
TkA04G458280	`PF23381`	Beta-prop_IFT122_1st	42	80	5.7e-21	75.8
TkA04G458280	`PF24817`	WD40_WDHD1_1st	42	124	4.3e-18	66.2
TkA04G458280	`PF29037`	DSE1_N	43	91	8.7e-13	48.8
TkA04G458280	`PF25391`	WD40_Gbeta	43	87	6.6e-10	39.2
TkA04G458280	`PF29630`	ASA1	43	151	0.0085	15.7
TkA04G458280	`PF24807`	WD40_CDC20-Fz	44	172	6.3e-37	128.2
TkA04G458280	`PF23215`	WD_LRWD1	44	95	5.9e-07	29.5
TkA04G458280	`PF23760`	Beta-prop_DCAF12	44	81	0.055	13.1
TkA04G458280	`PF24805`	EIF3I	45	127	1.2e-07	31.9
TkA04G458280	`PF25174`	Beta-prop_THOC3	52	152	5e-31	108.4

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
`O22467`	Arabidopsis thaliana	sp\|O22467\|MSI1_ARATH Histone-binding protein MSI1	58.400%	Swiss-Prot	High
`Q10G81`	Oryza sativa subsp. japonica	sp\|Q10G81\|MSI1_ORYSJ Histone-binding protein MSI1	56.200%	Swiss-Prot	High

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