LXL04_012640 | RubberDandelionOmics

Gene overview

LXL04_012640

Reference: OH-1004 Chr: Chr03 Coordinates: 16149960-16150517 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

558 bp · LXL04_012640|LXL04_012640|OH1004|cDNA

ATGGCTTCATCATCCAATCCTCCACAACTCCCTAAACTGACAAAAGGACGGCAAAAGATTGAAATGAAGAAAATCGATGATGAGAAAAAACTGAAGGTTTGTTTCTCAAAAAGGCATACTGGTCTTTTTAAAAAGGCGAATGAGTTATGCACCCTTTGTGGTGTAGAGATGGCAATAATCCTATTCTCCCCAACCAATAAGCCATTTTCATTTGGCCATCCATCTCTTCAGACGGTCATACATCGCTTCTTTCAGAACCA...

CDS

Download CDS FASTA

558 bp · LXL04_012640|LXL04_012640|OH1004|CDS

ATGGCTTCATCATCCAATCCTCCACAACTCCCTAAACTGACAAAAGGACGGCAAAAGATTGAAATGAAGAAAATCGATGATGAGAAAAAACTGAAGGTTTGTTTCTCAAAAAGGCATACTGGTCTTTTTAAAAAGGCGAATGAGTTATGCACCCTTTGTGGTGTAGAGATGGCAATAATCCTATTCTCCCCAACCAATAAGCCATTTTCATTTGGCCATCCATCTCTTCAGACGGTCATACATCGCTTCTTTCAGAACCA...

Protein

Download Protein FASTA

185 aa · LXL04_012640|LXL04_012640|OH1004|PROTEIN

MASSSNPPQLPKLTKGRQKIEMKKIDDEKKLKVCFSKRHTGLFKKANELCTLCGVEMAIILFSPTNKPFSFGHPSLQTVIHRFFQNQDPPAESSRTSELMQQYRDHRALELNTQFTNLQGQLEAAKKTGEELKKVRKARQEMFLWDAPLENLGEQELQKLKMAVLQLKKNAENQAYRNGGGVDGL

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_012640`
TK1151 ID	TkA02G547660
OH-1004 ID	LXL04_012640
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 88.649 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

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Basic Information and Functional Annotation

Gene ID LXL04_012640

Location Chr03:16149960-16150517 (+)

Description Similar to AGL62: Agamous-like MADS-box protein AGL62

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g60440`	Probable transcription factor.	The AGL62 MADS domain protein regulates cellularization during endosperm development in Arabidopsis.2008 · DOI: 10.1105/tpc.107.055137
`At2g24840`	Probable transcription factor.	AGL61 interacts with AGL80 and is required for central cell development in Arabidopsis.2008 · DOI: 10.1104/pp.108.119404 The MADS domain protein DIANA acts together with AGAMOUS-LIKE80 to specify the central cell in Arabidopsis ovules.2008 · DOI: 10.1105/tpc.108.058958
`At2g34440`	Probable transcription factor.	No verified direct reference in this release
`At1g01530`	Probable transcription factor that may function as a floral promoter operating upstream of known floral activators in the autonomous pathway.	Overexpression of AGAMOUS-LIKE 28 (AGL28) promotes flowering by upregulating expression of floral promoters within the autonomous pathway.2006 · DOI: 10.1016/j.bbrc.2006.07.121
`At1g65360`	Probable transcription factor that controls female gametophyte (megagametogenesis) development and chloroplast biogenesis during embryo development.	AGL23, a type I MADS-box gene that controls female gametophyte and embryo development in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03485.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012640 · 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:0009553 embryo sac development Biological Process

GO:0009559 embryo sac central cell differentiation Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009911 positive regulation of flower development Biological Process

GO:0009960 endosperm development Biological Process

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

GO:2000012 regulation of auxin polar transport Biological Process

GO:0005634 nucleus Cellular Component

GO:0043078 polar nucleus Cellular Component

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

KEGG gene cross-reference

ath:AT1G01530

ath:AT1G65360

ath:AT2G24840

ath:AT2G34440

ath:AT5G60440

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.

Nucleus0.970

Rank 1 · LXL04_012640 · OH-1004

Cytoplasm0.092

Rank 2 · LXL04_012640 · OH-1004

Cell membrane0.017

Rank 3 · LXL04_012640 · OH-1004

Endoplasmic reticulum0.012

Rank 4 · LXL04_012640 · OH-1004

Plastid0.008

Rank 5 · LXL04_012640 · 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-TF24-71 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012640	`PF00319.24`	SRF-TF	24	71	2.8e-23	81.8

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
`Q9FKK2`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL62	44.910%	Swiss-Prot	moderate database homology
`Q4PSU4`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL61	43.750%	Swiss-Prot	moderate database homology
`O64703`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL29	40.136%	Swiss-Prot	moderate database homology
`Q9LMM8`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL28	34.177%	Swiss-Prot	moderate database homology
`O80807`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL23	34.266%	Swiss-Prot	moderate database homology

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