LXL04_010406 | RubberDandelionOmics

Gene overview

LXL04_010406

Reference: OH-1004 Chr: Chr02 Coordinates: 146174492-146177488 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1938 bp · LXL04_010406|LXL04_010406|OH1004|cDNA

ATGGCAGATGGCCACTTATTCAACAACATATCTCTTGGAGGTCGTGGGGGCACAAATCCAGGCCAGCTTAAAGTTCATACAGGCGGCATATTATGGAAGAAACAAGGAGGTGGTAAGGCTATCGAAGTTGACAAGTCTGACATCTCGGGTCTTACCTGGATGAAAGTTCCCCGAACTAATCAGCTTGCTGTTAGAATCAAGGACGGTTTAAAGTACAAGTTCACTGGTTTTCGTGACCAGGATGTTATTAGCCTGACCAA...

CDS

Download CDS FASTA

1938 bp · LXL04_010406|LXL04_010406|OH1004|CDS

ATGGCAGATGGCCACTTATTCAACAACATATCTCTTGGAGGTCGTGGGGGCACAAATCCAGGCCAGCTTAAAGTTCATACAGGCGGCATATTATGGAAGAAACAAGGAGGTGGTAAGGCTATCGAAGTTGACAAGTCTGACATCTCGGGTCTTACCTGGATGAAAGTTCCCCGAACTAATCAGCTTGCTGTTAGAATCAAGGACGGTTTAAAGTACAAGTTCACTGGTTTTCGTGACCAGGATGTTATTAGCCTGACCAA...

Protein

Download Protein FASTA

645 aa · LXL04_010406|LXL04_010406|OH1004|PROTEIN

MADGHLFNNISLGGRGGTNPGQLKVHTGGILWKKQGGGKAIEVDKSDISGLTWMKVPRTNQLAVRIKDGLKYKFTGFRDQDVISLTNFFQNSCGLTTEEKQLSISGKNWGEVDLNGNSLSFLVGGKQAFEVSLADVSQTQLQGKNDVLLEFHVDDTTGANEKDSLMEISFHIPNNNTQFVGDEHRPPAQLFREKIMSMADVGAGGEEAVVTFEGIAILTPRGRYNVELHLSFLRLQGQANDFKIQFSSVVRVFVLPKSNQ...

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_010406`
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_010406

Location Chr02:146174492-146177488 (-)

Description Similar to SSRP1: FACT complex subunit SSRP1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g28730`	Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes.	The chromatin remodelling complex FACT associates with actively transcribed regions of the Arabidopsis genome.2004 · DOI: 10.1111/j.1365-313x.2004.02242.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0184900`	Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010406 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000741 karyogamy Biological Process

GO:0006260 DNA replication Biological Process

GO:0006281 DNA repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0010197 polar nucleus fusion Biological Process

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

GO:0048731 system development Biological Process

GO:0000791 euchromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0035101 FACT complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT3G28730

dosa:Os01g0184900

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.

Nucleus0.945

Rank 1 · LXL04_010406 · OH-1004

Cytoplasm0.160

Rank 2 · LXL04_010406 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_010406 · OH-1004

Mitochondrion0.015

Rank 4 · LXL04_010406 · OH-1004

Endoplasmic reticulum0.013

Rank 5 · LXL04_010406 · 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.

PF17292.9POB3_N7-98 aa

PF03531.22SSrecog102-194 aa

PF21103.4PH1_SSRP1-like207-335 aa

PF08512.19Rttp106-like_middle349-440 aa

PF09011.17HMG_box_2562-632 aa

PF00505.26HMG_box565-633 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010406	`PF17292.9`	POB3_N	7	98	9.3e-26	90.9
LXL04_010406	`PF03531.22`	SSrecog	102	194	1.2e-27	96.4
LXL04_010406	`PF21103.4`	PH1_SSRP1-like	207	335	1.3e-48	164.9
LXL04_010406	`PF08512.19`	Rttp106-like_middle	349	440	1.6e-24	86.8
LXL04_010406	`PF09011.17`	HMG_box_2	562	632	1.6e-14	55.1
LXL04_010406	`PF00505.26`	HMG_box	565	633	4.9e-21	75.7

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
`Q05153`	Arabidopsis thaliana	FACT complex subunit SSRP1	73.960%	Swiss-Prot	strong database homology
`Q9LGR0`	Oryza sativa subsp. japonica	FACT complex subunit SSRP1-A	69.066%	Swiss-Prot	strong database homology

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