LXL04_035470 | RubberDandelionOmics

Gene overview

LXL04_035470

Reference: OH-1004 Chr: Chr08 Coordinates: 23156455-23160233 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

876 bp · LXL04_035470|LXL04_035470|OH1004|cDNA

ATGGCGGATCACGACGACCACCATCAACAACACACCAGCTTGATTCACCACCTTCTAGACCCTCCTTCGCCAGAAGAAACCGACGGCAGTGGTGGTCCTACCCGCCGTTCACGTGGCCGCCCACCGGGCTCCAAAAACAAGCCAAAACCACCGGTTATCGTCACCCGTGACAGCCCCAACGCCCTTCGTTCTCACATTCTTGAGGTATCCGCCGGAGCCGACATCATTGAAAGCCTCTCCGTCTTCGCTCGCCGTAGAGG...

CDS

Download CDS FASTA

876 bp · LXL04_035470|LXL04_035470|OH1004|CDS

ATGGCGGATCACGACGACCACCATCAACAACACACCAGCTTGATTCACCACCTTCTAGACCCTCCTTCGCCAGAAGAAACCGACGGCAGTGGTGGTCCTACCCGCCGTTCACGTGGCCGCCCACCGGGCTCCAAAAACAAGCCAAAACCACCGGTTATCGTCACCCGTGACAGCCCCAACGCCCTTCGTTCTCACATTCTTGAGGTATCCGCCGGAGCCGACATCATTGAAAGCCTCTCCGTCTTCGCTCGCCGTAGAGG...

Protein

Download Protein FASTA

291 aa · LXL04_035470|LXL04_035470|OH1004|PROTEIN

MADHDDHHQQHTSLIHHLLDPPSPEETDGSGGPTRRSRGRPPGSKNKPKPPVIVTRDSPNALRSHILEVSAGADIIESLSVFARRRGRGVSVLSGTGAVEDVTLRQPADPSNNAVTLHGRFEILTLSGTVLPPPAPPNAGGLSVFLAGGGGQVVGGIPVGALVASSPVVLVAASFANAVFERLPLDEPEEDGGSAQVQPTASQCSGVTSGGGGVSVFNTAAAAGTNNSGSDYPFTGDTRKSTHNPILINFYSKRCDVMTE...

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_035470`
TK1151 ID	TkA04G128540
OH-1004 ID	LXL04_035470
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
Protein coverage (%)	TK1151 94.444 / OH-1004 81.787 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_035470

Location Chr08:23156455-23160233 (-)

Description Similar to AHL29: AT-hook motif nuclear-localized protein 29

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g76500`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity).	The AT-hook-containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2007.03393.x Over-expression of an AT-hook gene, AHL22, delays flowering and inhibits the elongation of the hypocotyl in Arabidopsis thaliana.2009 · DOI: 10.1007/s11103-009-9507-9
`At2g35270`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).	No verified direct reference in this release
`At1g20900`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).	Overexpression of a chromatin architecture-controlling AT-hook protein extends leaf longevity and increases the post-harvest storage life of plants.2007 · DOI: 10.1111/j.1365-313x.2007.03317.x The AT-hook-containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2007.03393.x Over-expression of an AT-hook gene, AHL22, delays flowering and inhibits the elongation of the hypocotyl in Arabidopsis thaliana.2009 · DOI: 10.1007/s11103-009-9507-9 Overexpression of AHL20 negatively regulates defenses in Arabidopsis.2010 · DOI: 10.1111/j.1744-7909.2010.00969.x
`At2g42940`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).	No verified direct reference in this release
`At4g14465`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity).	Overexpression of AHL20 negatively regulates defenses in Arabidopsis.2010 · DOI: 10.1111/j.1744-7909.2010.00969.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_035470 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009908 flower development Biological Process

GO:0010150 leaf senescence Biological Process

GO:0010208 pollen wall assembly Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0045087 innate immune response Biological Process

GO:0045824 negative regulation of innate immune response Biological Process

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

KEGG gene cross-reference

ath:AT1G20900

ath:AT1G76500

ath:AT2G35270

ath:AT2G42940

ath:AT4G14465

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.

Nucleus0.873

Rank 1 · LXL04_035470 · OH-1004

Cytoplasm0.193

Rank 2 · LXL04_035470 · OH-1004

Cell membrane0.044

Rank 3 · LXL04_035470 · OH-1004

Endoplasmic reticulum0.040

Rank 4 · LXL04_035470 · OH-1004

Plastid0.017

Rank 5 · LXL04_035470 · 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.

PF03479.22PCC57-175 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_035470	`PF03479.22`	PCC	57	175	3e-29	102.2

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
`Q9C9K7`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 29	66.477%	Swiss-Prot	moderate database homology
`O82166`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 21	59.239%	Swiss-Prot	moderate database homology
`Q9S7C9`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 27	64.550%	Swiss-Prot	moderate database homology
`Q9SJG4`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 16	63.871%	Swiss-Prot	moderate database homology
`Q8GWQ2`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 20	60.606%	Swiss-Prot	moderate database homology

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