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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

LXL04_009658
Reference: OH-1004 Chr: Chr02 Coordinates: 130811160-130812971 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1284 bp · LXL04_009658|LXL04_009658|OH1004|cDNA

ATTGCAGTTTGCCGCCATCTGATTTCTACTTCCAAACCTACGCGGGAACACAATCTAGAGTGTGAGGGAAAGAAAAGAATGAGGACGGAGGAAGACGAGGGCGCCGGCGAAGACATCCAAGTGGAGGAGGAGTTCAGTATATGGAAGAAGAACTCTCCGTTCTTATATGATCTCATCGTCTCCCACTCCCTTGAGTGGCCGTCGCTAACCGTTCATTGGCTCCCGTCACCACCAACTCCGTACAAAGACGGATCTTTCGC...

CDS

Download CDS FASTA

1266 bp · LXL04_009658|LXL04_009658|OH1004|CDS

CTGATTTCTACTTCCAAACCTACGCGGGAACACAATCTAGAGTGTGAGGGAAAGAAAAGAATGAGGACGGAGGAAGACGAGGGCGCCGGCGAAGACATCCAAGTGGAGGAGGAGTTCAGTATATGGAAGAAGAACTCTCCGTTCTTATATGATCTCATCGTCTCCCACTCCCTTGAGTGGCCGTCGCTAACCGTTCATTGGCTCCCGTCACCACCAACTCCGTACAAAGACGGATCTTTCGCCACTCACAAGTTGATTCT...

Protein

Download Protein FASTA

421 aa · LXL04_009658|LXL04_009658|OH1004|PROTEIN

MISTSKPTREHNLECEGKKRMRTEEDEGAGEDIQVEEEFSIWKKNSPFLYDLIVSHSLEWPSLTVHWLPSPPTPYKDGSFATHKLILGTHTSDESPNFLLVADVLLPVNPSSSLDTNHENPHTPKVDIVQKIHVDGEVNRARCMPQNPSIIAAKTSSSEVYVFDSTKQLLNDEGGSCEPDARLRGHEKEGYGLSWSPFKEGYLLSGSNDCKICLWDVSAMPSDKVLDAQHIYQDHGSLVEDVSWHLKNENLFGSVGDDCK...

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.

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ID Mapping

Input IDLXL04_009658
TK1151 IDTkA03G460550
OH-1004 IDLXL04_009658
Relationship / confidenceRbh 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 versionOH-1004 / GCA_047496595.1_OSU_TarKok_2.0
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDLXL04_009658
LocationChr02:130811160-130812971 (+)
DescriptionSimilar to MSI3: WD-40 repeat-containing protein MSI3
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / 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 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_009658 · GCA_047496595.1_OSU_TarKok_2.0.

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.

Nucleus0.873
Rank 1 · LXL04_009658 · OH-1004
Cytoplasm0.261
Rank 2 · LXL04_009658 · OH-1004
Cell membrane0.020
Rank 3 · LXL04_009658 · OH-1004
Mitochondrion0.020
Rank 4 · LXL04_009658 · OH-1004
Endoplasmic reticulum0.014
Rank 5 · LXL04_009658 · OH-1004

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.

PF12265.15CAF1C_H4-bd37-107 aa
PF23775.2Beta-prop_RIG_2nd130-225 aa
PF24796.2WDR55130-358 aa
PF24807.2WD40_CDC20-Fz134-264 aa
PF25173.2Beta-prop_WDR3_1st136-308 aa
PF24814.2WD40_Prp19137-313 aa
PF25174.2Beta-prop_THOC3155-220 aa
PF25047.1Beta-prop_TEP1_2nd156-282 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_009658PF12265.15CAF1C_H4-bd371074e-2691.8
LXL04_009658PF23775.2Beta-prop_RIG_2nd1302256.7e-1865.8
LXL04_009658PF24796.2WDR551303581.2e-1144.9
LXL04_009658PF24807.2WD40_CDC20-Fz1342642.6e-2899.9
LXL04_009658PF25173.2Beta-prop_WDR3_1st1363088.9e-35120.8
LXL04_009658PF24814.2WD40_Prp191373132.6e-2073.3
LXL04_009658PF25174.2Beta-prop_THOC31552202.9e-36125.6
LXL04_009658PF25047.1Beta-prop_TEP1_2nd1562823.9e-1246.6
LXL04_009658PF25175.2Beta-prop_WDR51782897.1e-2691.9
LXL04_009658PF23381.2Beta-prop_IFT122_1st1813544.8e-1762.9
LXL04_009658PF24105.2Beta-prop_CAF1B_HIR11822497.4e-2175.3
LXL04_009658PF25174.2Beta-prop_THOC31863112.9e-36125.6
LXL04_009658PF23414.2Beta-prop_EML_21913591.5e-1661.3
LXL04_009658PF25460.2Beta-prop_Aladin1923014e-1246.6
LXL04_009658PF23389.2Beta-prop_WDR19_1st1944112e-0627.8
LXL04_009658PF24817.2WD40_WDHD1_1st2033542.2e-1247.5

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
O22469Arabidopsis thalianaWD-40 repeat-containing protein MSI369.750%Swiss-Protstrong database homology
O22468Arabidopsis thalianaWD-40 repeat-containing protein MSI269.500%Swiss-Protstrong database homology
O22467Arabidopsis thalianaHistone-binding protein MSI158.794%Swiss-Protstrong database homology
Q10G81Oryza sativa subsp. japonicaHistone-binding protein MSI157.855%Swiss-Protstrong database homology

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