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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_008299
Reference: OH-1004 Chr: Chr02 Coordinates: 96072201-96076828 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1464 bp · LXL04_008299|LXL04_008299|OH1004|cDNA

ATGAAGGAAAGAGGCGGGAAAGGAGGAGGCCAGTCGTCGGTGAACGAGCGATACTCACAGTGGAAGACTCTCGTCCCCATTCTCTACGACTGGCTCGCCAACCACAACCTCGTTTGGCCCTCTCTTTCATGCCGATGGGGGCCACTACTTGAACAAGCTACTTACAAGAATCGCCAGCGCCTCTACCTCTCAGAACAGACTGATGGTAGTGTTCCAAACACACTTGTGATTGCAAATTGTGAAATTGTTAAACCAAGAGT...

CDS

Download CDS FASTA

1464 bp · LXL04_008299|LXL04_008299|OH1004|CDS

ATGAAGGAAAGAGGCGGGAAAGGAGGAGGCCAGTCGTCGGTGAACGAGCGATACTCACAGTGGAAGACTCTCGTCCCCATTCTCTACGACTGGCTCGCCAACCACAACCTCGTTTGGCCCTCTCTTTCATGCCGATGGGGGCCACTACTTGAACAAGCTACTTACAAGAATCGCCAGCGCCTCTACCTCTCAGAACAGACTGATGGTAGTGTTCCAAACACACTTGTGATTGCAAATTGTGAAATTGTTAAACCAAGAGT...

Protein

Download Protein FASTA

487 aa · LXL04_008299|LXL04_008299|OH1004|PROTEIN

MKERGGKGGGQSSVNERYSQWKTLVPILYDWLANHNLVWPSLSCRWGPLLEQATYKNRQRLYLSEQTDGSVPNTLVIANCEIVKPRVAAAEHIAQFNEEARSPFVKKFKTIIHPGEVNRIRELPQNSKIVATHTDSPDVLIWDVEAQPNRHAVLGATESRPDLILTGHQENAEFALAMCQSEPFVLSGGKDKSVVLWSIHDHISSLATESPGSNGPKTEDKVTESPKIQARGIYQGHSDTVEDVQFCPSSAQEFCSVGDD...

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_008299
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_008299
LocationChr02:96072201-96076828 (+)
DescriptionSimilar to MSI4: WD-40 repeat-containing protein MSI4
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g19520 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.
Regulation of flowering time by FVE, a retinoblastoma-associated protein.2004 · DOI: 10.1038/ng1295
A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana.2004 · DOI: 10.1038/ng1298
At4g29730 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 (By similarity).
Arabidopsis PWWP domain proteins mediate H3K27 trimethylation on FLC and regulate flowering time.2018 · DOI: 10.1111/jipb.12630
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

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_008299 · GCA_047496595.1_OSU_TarKok_2.0.

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:0006334 nucleosome assembly 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:0009627 systemic acquired resistance Biological Process
GO:0009908 flower development Biological Process
GO:0010224 response to UV-B Biological Process
GO:0010629 negative regulation of gene expression Biological Process
KEGG gene cross-reference
ath:AT2G16780
ath:AT2G19520
ath:AT4G29730
ddi:DDB_G0282529
mmu:19646
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.

Nucleus0.593
Rank 1 · LXL04_008299 · OH-1004
Cytoplasm0.447
Rank 2 · LXL04_008299 · OH-1004
Cell membrane0.054
Rank 3 · LXL04_008299 · OH-1004
Mitochondrion0.043
Rank 4 · LXL04_008299 · OH-1004
Lysosome / Vacuole0.041
Rank 5 · LXL04_008299 · 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-bd16-83 aa
PF24105.2Beta-prop_CAF1B_HIR1127-315 aa
PF25175.2Beta-prop_WDR5227-364 aa
PF25047.1Beta-prop_TEP1_2nd227-368 aa
PF23775.2Beta-prop_RIG_2nd228-303 aa
PF25391.2WD40_Gbeta229-314 aa
PF24805.2EIF3I232-364 aa
PF25174.2Beta-prop_THOC3233-314 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_008299PF12265.15CAF1C_H4-bd16833.9e-2072.6
LXL04_008299PF24105.2Beta-prop_CAF1B_HIR11273153.4e-1556.6
LXL04_008299PF25175.2Beta-prop_WDR52273645.4e-2692.3
LXL04_008299PF25047.1Beta-prop_TEP1_2nd2273683.6e-1246.7
LXL04_008299PF23775.2Beta-prop_RIG_2nd2283031.6e-1144.9
LXL04_008299PF25391.2WD40_Gbeta2293141.8e-0834.5
LXL04_008299PF24805.2EIF3I2323643.1e-0627.3
LXL04_008299PF25174.2Beta-prop_THOC32333144.5e-2588.9
LXL04_008299PF24817.2WD40_WDHD1_1st2333637.5e-0935.9
LXL04_008299PF23381.2Beta-prop_IFT122_1st2342942.8e-1970.3
LXL04_008299PF24807.2WD40_CDC20-Fz2343644e-1969.7
LXL04_008299PF24796.2WDR552343632.3e-1040.7
LXL04_008299PF25173.2Beta-prop_WDR3_1st2353122e-2074.0
LXL04_008299PF23609.2Beta-prop_EIPR12353112.1e-1557.6
LXL04_008299PF25172.2Beta-prop_WDR3_2nd2353142.4e-1144.1
LXL04_008299PF23393.3Beta-prop_WDR90_POC16_2nd2353569e-0625.8

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
O22607Arabidopsis thalianaWD-40 repeat-containing protein MSI479.318%Swiss-Protstrong database homology
Q9SU78Arabidopsis thalianaWD-40 repeat-containing protein MSI572.727%Swiss-Protstrong database homology
O22468Arabidopsis thalianaWD-40 repeat-containing protein MSI232.294%Swiss-Protmoderate database homology

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