RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

TkA04G456600
Reference: TK1151 Chr: Chr04 Coordinates: 115102698-115106625 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2147 bp · TkA04G456600|TK1151|cDNA

GCCATGGTCTTTTTTTGGAGCGTTTTGAAAAGACTGATGGATTATTTTGGGGCGGTTCGTCACGCAATACAAGTCTTTTTATGTCATTTGAATTTCAAAGAGACTCCGAAACCATACTCCATTGAGAGGGGAGATAGACTGCCGATCAAAGATTAGATACGGTTCTTGCTACGATTGGTGATTAACGACGCGCCTGAGTGACTGTAGCGCACCGTGGAATGGTTCCAAGATCGTGACGAACATGCTAGAAACTACCATTT...

CDS

Download CDS FASTA

1287 bp · TkA04G456600|TK1151|CDS

ATGAAGATGGAGGCCGAAAAGGACACAAATCTTGAACACAAGGAGGATGAAAAAGGGGATGAAGAAACAAGAGTCGACATAGAGGATTCAAGGGGGGAAATAGTTGAGAGGTTGGTTAACGAAGAGTACAAAATTTGGAAAAAAGAAACTCCATTTTTGTACGATTTGGTCATTTCACATGCACTTGAGTGGCCTTCACTCACAGTCGAGTGGATCCCTGACCGGGTAGAATCTTCAGACAAGGGCGTATCCGTCCAAAA...

Protein

Download Protein FASTA

428 aa · TkA04G456600|TK1151|PROTEIN

MKMEAEKDTNLEHKEDEKGDEETRVDIEDSRGEIVERLVNEEYKIWKKETPFLYDLVISHALEWPSLTVEWIPDRVESSDKGVSVQKLIFGTHTTDNEPNYLVISEVKLPLFDVDYDSSDNEDECVGRKIEVVQQIYHEGEVHRARYMPQNYSIIATKSVHSDVFVFASEFHPIKPFPDENETCNPDLRLRGHENDGFGLSWSKFKEGWLLSGSYDGKICMWDINGTPEDQAIDAMQVYKVHNAPVEDVAWSLRHDYLFA...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDTkA04G456600
TK1151 IDTkA04G456600
OH-1004 IDLXL04_038714
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)99.500
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 versionTK1151 / 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 IDTkA04G456600
LocationChr04:115102698-115106625 (+)
DescriptionSimilar to MSI1: WD-40 repeat-containing protein MSI1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / 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 IDPossible functionPapers / 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.

Nucleus0.790
Rank 1 · TkA04G456600 · TK1151
Cytoplasm0.359
Rank 2 · TkA04G456600 · TK1151
Cell membrane0.022
Rank 3 · TkA04G456600 · TK1151
Mitochondrion0.021
Rank 4 · TkA04G456600 · TK1151
Lysosome / Vacuole0.017
Rank 5 · TkA04G456600 · 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.

PF00703Glyco_hydro_211-59 aa
PF12265CAF1C_H4-bd41-110 aa
PF23770Beta-prop_RIG_1st118-150 aa
PF24807WD40_CDC20-Fz126-263 aa
PF24105Beta-prop_CAF1B_HIR1131-275 aa
PF20426NBCH_WD40131-168 aa
PF25171Beta-prop_WDR36-Utp21_1st135-155 aa
PF23775Beta-prop_RIG_2nd140-229 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G456600PF00703Glyco_hydro_211590.08114.4
TkA04G456600PF12265CAF1C_H4-bd411101.2e-2899.8
TkA04G456600PF23770Beta-prop_RIG_1st1181500.007715.6
TkA04G456600PF24807WD40_CDC20-Fz1262636.9e-29101.8
TkA04G456600PF24105Beta-prop_CAF1B_HIR11312759.4e-1968.3
TkA04G456600PF20426NBCH_WD401311680.01315.1
TkA04G456600PF25171Beta-prop_WDR36-Utp21_1st1351552.1e-0938.0
TkA04G456600PF23775Beta-prop_RIG_2nd1402294.9e-1866.3
TkA04G456600PF25175Beta-prop_WDR51642254.7e-2795.7
TkA04G456600PF23869Beta-prop_WDR75_1st1722243.1e-0524.1
TkA04G456600PF24805EIF3I1792742.8e-0730.7
TkA04G456600PF25173Beta-prop_WDR3_1st1803191.3e-2281.1
TkA04G456600PF23381Beta-prop_IFT122_1st1892275.1e-2072.7
TkA04G456600PF25168Beta-prop_WDR36-Utp21_2nd1892411.5e-1041.6
TkA04G456600PF24817WD40_WDHD1_1st1902711.7e-1867.6
TkA04G456600PF29037DSE1_N1902387.5e-1245.7

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
O22467Arabidopsis thalianasp|O22467|MSI1_ARATH Histone-binding protein MSI158.900%Swiss-ProtHigh
Q10G81Oryza sativa subsp. japonicasp|Q10G81|MSI1_ORYSJ Histone-binding protein MSI156.500%Swiss-ProtHigh

JBrowse

View in Genome Browser