LXL04_032750 | RubberDandelionOmics

Gene overview

LXL04_032750

Reference: OH-1004 Chr: Chr07 Coordinates: 28980477-28988721 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5832 bp · LXL04_032750|LXL04_032750|OH1004|cDNA

ATGGCCTCTAAAGGTCCAAGGTCTAGACTTGATCATGAGACAAGAGCCAAACGGCAAAAGGCTCTTGAACCACCCAAGGAACCCCAGCGGCCCAGAACTCATTGGGACCATCTTTTGGAAGAGATGGTATGGTTATCAAAGGATTTCGAGTCTGAGAGAAAATTCAAATTAGGCCTGGCAAAAAGGATTGCCATAAGGGCCAGCAAAGGTATGGTAGATCAAGCCACAAAAGGTGAAAGAAGAGTGAAGGAGGAAGAGCT...

CDS

Download CDS FASTA

5832 bp · LXL04_032750|LXL04_032750|OH1004|CDS

ATGGCCTCTAAAGGTCCAAGGTCTAGACTTGATCATGAGACAAGAGCCAAACGGCAAAAGGCTCTTGAACCACCCAAGGAACCCCAGCGGCCCAGAACTCATTGGGACCATCTTTTGGAAGAGATGGTATGGTTATCAAAGGATTTCGAGTCTGAGAGAAAATTCAAATTAGGCCTGGCAAAAAGGATTGCCATAAGGGCCAGCAAAGGTATGGTAGATCAAGCCACAAAAGGTGAAAGAAGAGTGAAGGAGGAAGAGCT...

Protein

Download Protein FASTA

1943 aa · LXL04_032750|LXL04_032750|OH1004|PROTEIN

MASKGPRSRLDHETRAKRQKALEPPKEPQRPRTHWDHLLEEMVWLSKDFESERKFKLGLAKRIAIRASKGMVDQATKGERRVKEEELRMKKVALNISKDVKKFWTKIEKLVLYKHRLELDQKKKKALDKQLEFLLGQTERYSTMLAENLVDSSSRQHVNLPPVPAIEYKDQSDVNGSAEPNVESQSNILETDEDYKSEIEPEDDEHTLEEDEALITEDERREEIAALQNEMDLPLEELLSRYTAKDEETTPGKTEGVAEV...

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_032750`
TK1151 ID	TkA08G203200
OH-1004 ID	LXL04_032750
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
Protein coverage (%)	TK1151 99.454 / OH-1004 93.824 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_032750

Location Chr07:28980477-28988721 (-)

Description Similar to PIE1: Protein PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g12810`	Component of the SWR1 complex which mediates the ATP- dependent exchange of histone H2A for the H2A variant H2A.F/Z leading to transcriptional regulation of selected genes (e.g. FLC) by chromatin remodeling.	PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis.2003 · DOI: 10.1105/tpc.012161 Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z.2007 · DOI: 10.1105/tpc.106.048447 Histone H2A.Z and homologues of components of the SWR1 complex are required to control immunity in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2007.03361.x

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_032750 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000725 recombinational repair Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009908 flower development Biological Process

GO:0030154 cell differentiation Biological Process

GO:0045815 transcription initiation-coupled chromatin remodeling Biological Process

GO:0046686 response to cadmium ion Biological Process

GO:1900239 regulation of phenotypic switching Biological Process

GO:0000785 chromatin Cellular Component

GO:0000812 Swr1 complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT3G12810

cal:CAALFM_C207560WA

cgr:2891166

kla:KLLA0_F21758g

sce:YDR334W

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.

Nucleus0.945

Rank 1 · LXL04_032750 · OH-1004

Cytoplasm0.129

Rank 2 · LXL04_032750 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_032750 · OH-1004

Mitochondrion0.017

Rank 4 · LXL04_032750 · OH-1004

Endoplasmic reticulum0.009

Rank 5 · LXL04_032750 · 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.

PF07529.19HSA26-92 aa

PF04851.22ResIII463-624 aa

PF00176.30SNF2-rel_dom468-753 aa

PF00270.36DEAD485-625 aa

PF00271.38Helicase_C992-1104 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032750	`PF07529.19`	HSA	26	92	2.6e-13	50.8
LXL04_032750	`PF04851.22`	ResIII	463	624	4.5e-12	46.9
LXL04_032750	`PF00176.30`	SNF2-rel_dom	468	753	3.1e-90	302.9
LXL04_032750	`PF00270.36`	DEAD	485	625	8.7e-09	36.1
LXL04_032750	`PF00271.38`	Helicase_C	992	1104	1.6e-27	96.6

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
`Q7X9V2`	Arabidopsis thaliana	Protein PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1	57.102%	Swiss-Prot	strong database homology

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