LXL04_025609 | RubberDandelionOmics

Gene overview

LXL04_025609

Reference: OH-1004 Chr: Chr05 Coordinates: 114182179-114182901 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

723 bp · LXL04_025609|LXL04_025609|OH1004|cDNA

ATGACTAGGAAGAAAGTCAAGCTTGCCTTCATAACCAACGACTCATCAAGGAAAGCAACcttcaagaaaaggaagaaagGTTTGATGAAGAAAGTGAACGAGTTGAGTACCTTATGCGGCATTGATGCATGCGCCATCATATACAGCCCATATGAAACTCAACCCGAGATCTGGCCCAACAACCTCGGCGTCCAACATGTGCTTGCTCAATTTAAGAAGGTCTCTGAAATGGATAGAAGCAAGAACATGCTGAATCAGGA...

CDS

Download CDS FASTA

723 bp · LXL04_025609|LXL04_025609|OH1004|CDS

ATGACTAGGAAGAAAGTCAAGCTTGCCTTCATAACCAACGACTCATCAAGGAAAGCAACCTTCAAGAAAAGGAAGAAAGGTTTGATGAAGAAAGTGAACGAGTTGAGTACCTTATGCGGCATTGATGCATGCGCCATCATATACAGCCCATATGAAACTCAACCCGAGATCTGGCCCAACAACCTCGGCGTCCAACATGTGCTTGCTCAATTTAAGAAGGTCTCTGAAATGGATAGAAGCAAGAACATGCTGAATCAGGA...

Protein

Download Protein FASTA

240 aa · LXL04_025609|LXL04_025609|OH1004|PROTEIN

MTRKKVKLAFITNDSSRKATFKKRKKGLMKKVNELSTLCGIDACAIIYSPYETQPEIWPNNLGVQHVLAQFKKVSEMDRSKNMLNQESFIRKQIGKANEQLKKQMKENREKEMTEVMYQCLTGKGSLENLSLADLKDLGGLVDQTLNDISRRIESLKNGGSSSNSVDGVTKRGVAMNAPEKQAMVDGNVSGVNGIQRTQWFTDWMSNPSEENLGVGNGYGIAQFVENSNRMWPHPFFPEG

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_025609`
TK1151 ID	TkA06G049290
OH-1004 ID	LXL04_025609
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_025609

Location Chr05:114182179-114182901 (-)

Description Similar to AGL80: Agamous-like MADS-box protein AGL80

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g48670`	Probable transcription factor.	AGL80 is required for central cell and endosperm development in Arabidopsis.2006 · DOI: 10.1105/tpc.106.040824
`At1g65330`	Probable transcription factor involved in the development of gametophytes and seeds.	The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1.2003 · DOI: 10.1101/gad.257403
`At1g65300`	Probable transcription factor involved in the development of gametophytes and seeds.	No verified direct reference in this release
`At5g26650`	Probable transcription factor.	No verified direct reference in this release
`At1g31640`	Putative transcription factor.	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_025609 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process

GO:0005634 nucleus Cellular Component

GO:0043078 polar nucleus Cellular Component

GO:0090406 pollen tube Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding Molecular Function

GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0046983 protein dimerization activity Molecular Function

KEGG gene cross-reference

ath:AT1G31640

ath:AT1G65300

ath:AT1G65330

ath:AT5G26650

ath:AT5G48670

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.

Nucleus0.977

Rank 1 · LXL04_025609 · OH-1004

Cytoplasm0.075

Rank 2 · LXL04_025609 · OH-1004

Cell membrane0.017

Rank 3 · LXL04_025609 · OH-1004

Endoplasmic reticulum0.011

Rank 4 · LXL04_025609 · OH-1004

Plastid0.008

Rank 5 · LXL04_025609 · 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.

PF00319.24SRF-TF10-51 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025609	`PF00319.24`	SRF-TF	10	51	5.5e-19	68.1

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
`Q9FJK3`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL80	54.146%	Swiss-Prot	strong database homology
`O80805`	Arabidopsis thaliana	MADS-box transcription factor PHERES 1	46.667%	Swiss-Prot	moderate database homology
`Q7XJK8`	Arabidopsis thaliana	MADS-box transcription factor PHERES 2	46.951%	Swiss-Prot	moderate database homology
`Q7XJK6`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL36	39.796%	Swiss-Prot	moderate database homology
`Q9C6V4`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL92	43.293%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card