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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_009286
Reference: OH-1004 Chr: Chr02 Coordinates: 122022538-122025405 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1578 bp · LXL04_009286|LXL04_009286|OH1004|cDNA

ATGGCTGCTAGCGACATTGGCGACGAGACGAGCGACATGGACGAGCAAGAGCAAGAAGAGGCTTTGGTGGCTTTAATCGAACACCGTACCAAAGAAGTTGAACATCTCCGTATGCGTGTAGCCTATTATGAATCCGAGCTTGTTGAATCTGAGAAAAAATTGGAGGAAACACAAGGCCAATTGGCTCGCCTTCGAAGTCGAGCATCTACAAGATCAATTGGAAGCAGTATAAgagttaaagaagaaatatcAACTAGTCC...

CDS

Download CDS FASTA

1578 bp · LXL04_009286|LXL04_009286|OH1004|CDS

ATGGCTGCTAGCGACATTGGCGACGAGACGAGCGACATGGACGAGCAAGAGCAAGAAGAGGCTTTGGTGGCTTTAATCGAACACCGTACCAAAGAAGTTGAACATCTCCGTATGCGTGTAGCCTATTATGAATCCGAGCTTGTTGAATCTGAGAAAAAATTGGAGGAAACACAAGGCCAATTGGCTCGCCTTCGAAGTCGAGCATCTACAAGATCAATTGGAAGCAGTATAAGAGTTAAAGAAGAAATATCAACTAGTCC...

Protein

Download Protein FASTA

525 aa · LXL04_009286|LXL04_009286|OH1004|PROTEIN

MAASDIGDETSDMDEQEQEEALVALIEHRTKEVEHLRMRVAYYESELVESEKKLEETQGQLARLRSRASTRSIGSSIRVKEEISTSPLKITNDKPSDKSNGTSCDSKTIKTKPKPLLVIPGMNPKASQSAPLKMVEYDKASSQRESQGYGVLTKQEAAESQAKGTKRKRKSKENGHKDLSEVICSCSSPITITAISHHIPSQHKRKLRSLVLCPTNDQLFATSALDGIVNMWQIEGRGSHAQLVNSINVASLTQRRWPED...

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_009286
TK1151 IDTkA03G415860
OH-1004 IDLXL04_009286
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)99.600
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 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_009286
LocationChr02:122022538-122025405 (-)
DescriptionSimilar to MSI1: Histone-binding 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_009286 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process
GO:0000209 protein polyubiquitination 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:0006511 ubiquitin-dependent protein catabolic process Biological Process
GO:0006513 protein monoubiquitination Biological Process
KEGG gene cross-reference
ath:AT5G58230
dme:Dmel_CG4236
dosa:Os03g0640100
gga:395390
xtr:395039
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.

Nucleus0.800
Rank 1 · LXL04_009286 · OH-1004
Cytoplasm0.233
Rank 2 · LXL04_009286 · OH-1004
Cell membrane0.040
Rank 3 · LXL04_009286 · OH-1004
Lysosome / Vacuole0.027
Rank 4 · LXL04_009286 · OH-1004
Golgi apparatus0.023
Rank 5 · LXL04_009286 · 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.

PF24817.2WD40_WDHD1_1st183-339 aa
PF25174.2Beta-prop_THOC3201-299 aa
PF25175.2Beta-prop_WDR5203-379 aa
PF24807.2WD40_CDC20-Fz279-432 aa
PF25173.2Beta-prop_WDR3_1st279-431 aa
PF24814.2WD40_Prp19292-481 aa
PF24796.2WDR55310-441 aa
PF25174.2Beta-prop_THOC3319-446 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_009286PF24817.2WD40_WDHD1_1st1833391e-1765.0
LXL04_009286PF25174.2Beta-prop_THOC32012993.5e-2486.0
LXL04_009286PF25175.2Beta-prop_WDR52033793.6e-1660.0
LXL04_009286PF24807.2WD40_CDC20-Fz2794321.3e-1558.2
LXL04_009286PF25173.2Beta-prop_WDR3_1st2794311.7e-1557.9
LXL04_009286PF24814.2WD40_Prp192924818.5e-1968.4
LXL04_009286PF24796.2WDR553104419.9e-1038.7
LXL04_009286PF25174.2Beta-prop_THOC33194463.5e-2486.0
LXL04_009286PF24807.2WD40_CDC20-Fz3455061.3e-1558.2
LXL04_009286PF24817.2WD40_WDHD1_1st3555071e-1765.0
LXL04_009286PF23381.2Beta-prop_IFT122_1st3555235.8e-1762.6
LXL04_009286PF25168.2Beta-prop_WDR36-Utp21_2nd3554811.8e-0834.8
LXL04_009286PF24782.3WD40_MABP1-WDR62_2nd3575174.4e-1039.8
LXL04_009286PF24805.2EIF3I3575205.9e-0832.9
LXL04_009286PF23414.2Beta-prop_EML_23625201.3e-1661.5
LXL04_009286PF25173.2Beta-prop_WDR3_1st4175191.7e-1557.9

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 thalianaHistone-binding protein MSI130.159%Swiss-Protweak database homology
Q10G81Oryza sativa subsp. japonicaHistone-binding protein MSI130.137%Swiss-Protweak database homology

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