LXL04_019515 | RubberDandelionOmics

Gene overview

LXL04_019515

Reference: OH-1004 Chr: Chr04 Coordinates: 32816346-32819921 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1491 bp · LXL04_019515|LXL04_019515|OH1004|cDNA

ATGATGGGCGGCGTGACTGGACGGCGGCAAGGGGAGGAGATTCTGAGACGAATTGCTCTTCTTGTATATGTATTTTTTCGGGATTCCGGGGAATTGCTCCCAAGAAAAGGGGAGGGGATGCCGAGATATCGAAGTGGGGTGGATGGGATAGGAGTTGTGACAGAAAAATCATCGGACATGGAGTCTGAGAACGAGAGAGATTTGATCCGGCGAGAGTGTTGGGGGATATCCTTAGAAGCCATTGATGTTTTTTTGGGAGA...

CDS

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1491 bp · LXL04_019515|LXL04_019515|OH1004|CDS

ATGATGGGCGGCGTGACTGGACGGCGGCAAGGGGAGGAGATTCTGAGACGAATTGCTCTTCTTGTATATGTATTTTTTCGGGATTCCGGGGAATTGCTCCCAAGAAAAGGGGAGGGGATGCCGAGATATCGAAGTGGGGTGGATGGGATAGGAGTTGTGACAGAAAAATCATCGGACATGGAGTCTGAGAACGAGAGAGATTTGATCCGGCGAGAGTGTTGGGGGATATCCTTAGAAGCCATTGATGTTTTTTTGGGAGA...

Protein

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496 aa · LXL04_019515|LXL04_019515|OH1004|PROTEIN

MMGGVTGRRQGEEILRRIALLVYVFFRDSGELLPRKGEGMPRYRSGVDGIGVVTEKSSDMESENERDLIRRECWGISLEAIDVFLGEDQTKSYLPNFCLIFLLATLGFLLHPLMESTTSSHEVLICQTCGDKGFTNAFIYCVKCLGFVVHRYCLHVITFDEFVHWVCEDCQQPLPIPSTSQSHKLNPKPNATSSPTIKPSKRKKRSKIPKKKRKIAPFVEERKEEESQGGFKTFVLALEAQTKGEKERKIDENVEILKED...

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	`LXL04_019515`
TK1151 ID	TkA05G057570
OH-1004 ID	LXL04_019515
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.700
Protein coverage (%)	TK1151 92.991 / OH-1004 80.242 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_019515

Location Chr04:32816346-32819921 (-)

Description Protein of unknown function

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g43770`	Together with AIPP3/BDT1, cooperates to form a BAH-PHD bivalent histone reader complex able to read histone H3 lysine 27 trimethylation (H3K27me3) histone marks in order to regulate transcription, especially to prevent early flowering; promotes AIPP3/BDT1 binding to H3K27me3.	A histone H3K27me3 reader cooperates with a family of PHD finger-containing proteins to regulate flowering time in Arabidopsis.2021 · DOI: 10.1111/jipb.13067
`At3g02890`	Together with AIPP3/BDT1 and PAIPP2, cooperates to form a BAH-PHD bivalent histone reader complex able to read histone H3 lysine 27 trimethylation (H3K27me3) and low-methylated H3K4 histone marks in order to regulate transcription, especially to prevent early flowering; promotes AIPP3/BDT1 binding to H3K27me3.	A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis .2017 · DOI: 10.1073/pnas.1710683114 Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis.2020 · DOI: 10.1038/s41467-020-20089-0
`At5g16680`	Together with AIPP2 and AIPP3/BDT1, cooperates to form a BAH-PHD bivalent histone reader complex able to read histone H3 lysine 27 trimethylation (H3K27me3) and low-methylated H3K4 histone marks in order to regulate transcription, especially to prevent early flowering; promotes AIPP3/BDT1 binding to H3K27me3.	Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis.2020 · DOI: 10.1038/s41467-020-20089-0
`At5g61120`	Together with AIPP3/BDT1, cooperates to form a BAH-PHD bivalent histone reader complex able to read histone H3 lysine 27 trimethylation (H3K27me3) histone marks in order to regulate transcription, especially to prevent early flowering; promotes AIPP3/BDT1 binding to H3K27me3.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_019515 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0034244 negative regulation of transcription elongation by RNA polymerase II Biological Process

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0042393 histone binding Molecular Function

GO:0061628 histone H3K27me3 reader activity Molecular Function

GO:0140566 histone reader activity Molecular Function

KEGG gene cross-reference

ath:AT1G43770

ath:AT5G16680

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.916

Rank 1 · LXL04_019515 · OH-1004

Cytoplasm0.140

Rank 2 · LXL04_019515 · OH-1004

Cell membrane0.041

Rank 3 · LXL04_019515 · OH-1004

Endoplasmic reticulum0.024

Rank 4 · LXL04_019515 · OH-1004

Plastid0.014

Rank 5 · LXL04_019515 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF23121.2SPOC_AIPP2332-460 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019515	`PF23121.2`	SPOC_AIPP2	332	460	5.4e-45	153.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`B3H578`	Arabidopsis thaliana	PHD finger-containing protein 1	39.860%	Swiss-Prot	weak database homology
`F4IYH6`	Arabidopsis thaliana	ASI1-immunoprecipitated protein 2	34.437%	Swiss-Prot	weak database homology
`F4KE59`	Arabidopsis thaliana	Protein PARALOG OF AIPP2	35.443%	Swiss-Prot	weak database homology
`F4K200`	Arabidopsis thaliana	PHD finger-containing protein 6	26.190%	Swiss-Prot	weak database homology

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