LXL04_011520 | RubberDandelionOmics

Gene overview

LXL04_011520

Reference: OH-1004 Chr: Chr02 Coordinates: 166061636-166065958 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2451 bp · LXL04_011520|LXL04_011520|OH1004|cDNA

ATGCTTATAACTGCCATCTTTACTAATGCACTTGAAGATTCTGTCACTGAACTATTTCATCAAGATATGCGTGATCAAGTGATTTGTCTCCATGAAAAGGTGAAAGAAAGATTACATAACTCAGATGATTACCAATCATTCTTGAAATGCATTGTGCATTATTGCACAGAAAATATTAACCGACCACAGCTGCAATCCCTGGTGAATAATTTACTTGGAGCTCACCCAGATCTTATGGAAGAAGTCAACGGGTTCATTGA...

CDS

Download CDS FASTA

2451 bp · LXL04_011520|LXL04_011520|OH1004|CDS

ATGCTTATAACTGCCATCTTTACTAATGCACTTGAAGATTCTGTCACTGAACTATTTCATCAAGATATGCGTGATCAAGTGATTTGTCTCCATGAAAAGGTGAAAGAAAGATTACATAACTCAGATGATTACCAATCATTCTTGAAATGCATTGTGCATTATTGCACAGAAAATATTAACCGACCACAGCTGCAATCCCTGGTGAATAATTTACTTGGAGCTCACCCAGATCTTATGGAAGAAGTCAACGGGTTCATTGA...

Protein

Download Protein FASTA

816 aa · LXL04_011520|LXL04_011520|OH1004|PROTEIN

MLITAIFTNALEDSVTELFHQDMRDQVICLHEKVKERLHNSDDYQSFLKCIVHYCTENINRPQLQSLVNNLLGAHPDLMEEVNGFIDRSERTDDEDKNVSESNKPSSLPNKDEYEAKPIHELDLSDCERCTPSYRLLPKNYPIPSVSQRTKIGVEVLNDHWVSVTSGSEDYSFKHMRKNQYEESLFRCEDDRFELDMLLESVNITAKRVEELLDKVNDNSIKTESVVRIEDHFTDNGLDVMDVLKKNASLALPVILTRLR...

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_011520`
TK1151 ID	TkA03G596460
OH-1004 ID	LXL04_011520
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	94.600
Protein coverage (%)	TK1151 77.083 / OH-1004 18.260 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011520

Location Chr02:166061636-166065958 (+)

Description Similar to SNL3: Paired amphipathic helix protein Sin3-like 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g24190`	Acts as a transcriptional repressor.	Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses.2005 · DOI: 10.1105/tpc.105.033043
`At1g70060`	Acts as a transcriptional repressor.	No verified direct reference in this release
`At5g15020`	Acts as a transcriptional repressor.	No verified direct reference in this release
`At3g01320`	Acts as a transcriptional repressor.	PAH-domain-specific interactions of the Arabidopsis transcription coregulator SIN3-LIKE1 (SNL1) with telomere-binding protein 1 and ALWAYS EARLY2 Myb-DNA binding factors.2010 · DOI: 10.1016/j.jmb.2009.11.065
`At1g59890`	Acts as a transcriptional repressor.	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_011520 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0000118 histone deacetylase complex Cellular Component

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0070822 Sin3-type complex Cellular Component

GO:0003714 transcription corepressor activity Molecular Function

KEGG gene cross-reference

ath:AT1G24190

ath:AT1G70060

ath:AT5G15020

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.

Nucleus0.775

Rank 1 · LXL04_011520 · OH-1004

Cytoplasm0.245

Rank 2 · LXL04_011520 · OH-1004

Cell membrane0.046

Rank 3 · LXL04_011520 · OH-1004

Mitochondrion0.023

Rank 4 · LXL04_011520 · OH-1004

Golgi apparatus0.020

Rank 5 · LXL04_011520 · 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.

PF02671.27PAH43-85 aa

PF08295.18Sin3_corepress128-220 aa

PF16879.11Sin3a_C527-771 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011520	`PF02671.27`	PAH	43	85	7.4e-11	42.3
LXL04_011520	`PF08295.18`	Sin3_corepress	128	220	3.4e-35	120.7
LXL04_011520	`PF16879.11`	Sin3a_C	527	771	4.2e-38	132.2

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

Protein	Organism	Description	Identity	Database	Confidence
`O48686`	Arabidopsis thaliana	Paired amphipathic helix protein Sin3-like 3	55.916%	Swiss-Prot	weak database homology
`O04539`	Arabidopsis thaliana	Paired amphipathic helix protein Sin3-like 4	43.118%	Swiss-Prot	moderate database homology
`Q9LFQ3`	Arabidopsis thaliana	Paired amphipathic helix protein Sin3-like 2	50.585%	Swiss-Prot	weak database homology
`Q9SRH9`	Arabidopsis thaliana	Paired amphipathic helix protein Sin3-like 1	48.352%	Swiss-Prot	moderate database homology
`Q9XIE1`	Arabidopsis thaliana	Paired amphipathic helix protein Sin3-like 5	62.126%	Swiss-Prot	weak database homology

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