LXL04_026790 | RubberDandelionOmics

Gene overview

LXL04_026790

Reference: OH-1004 Chr: Chr06 Coordinates: 2917764-2921315 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

657 bp · LXL04_026790|LXL04_026790|OH1004|cDNA

ATGGTGAGAGGGAAGACTCAAATGCGAAGGATTGAAAATGCTACAAGTAGACAAGTGACCTTCTCCAAAAGAAGAAATGGTTTGTTGAAAAAAGCGTTCGAACTCTCTGTGCTTTGTGATGCTGAAGTTGCTTTGATAATCTTCTCTCCAAGAGGCAAACTTTATGAATTTGCAAGCTCAAGCATGCAGGAGACTATAGAACGATATAGAAGTCATGTAAAAGATATTCAAGCAGACAATTCTTCAAGTGTAGAAGATGT...

CDS

Download CDS FASTA

657 bp · LXL04_026790|LXL04_026790|OH1004|CDS

ATGGTGAGAGGGAAGACTCAAATGCGAAGGATTGAAAATGCTACAAGTAGACAAGTGACCTTCTCCAAAAGAAGAAATGGTTTGTTGAAAAAAGCGTTCGAACTCTCTGTGCTTTGTGATGCTGAAGTTGCTTTGATAATCTTCTCTCCAAGAGGCAAACTTTATGAATTTGCAAGCTCAAGCATGCAGGAGACTATAGAACGATATAGAAGTCATGTAAAAGATATTCAAGCAGACAATTCTTCAAGTGTAGAAGATGT...

Protein

Download Protein FASTA

218 aa · LXL04_026790|LXL04_026790|OH1004|PROTEIN

MVRGKTQMRRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFASSSMQETIERYRSHVKDIQADNSSSVEDVQHLKQETATMAKKVELLEVAKRKLLGEGLGSSTVDEIVQVEQQLERSVRIIRARKMQVYNEQIEQLQAKEKMLAAENATLTEKCLIHTDQGTEEIRPDLRVVDNGENSDVETELFIGPPEIRRTIKQRWLN

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_026790`
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_026790

Location Chr06:2917764-2921315 (+)

Description Similar to SOC1: MADS-box protein SOC1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g45660`	May participate in transcriptional regulation of flowering time and floral development.	The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis.2000 · DOI: 10.1101/gad.813600 Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis.2008 · DOI: 10.1242/dev.020255 The Arabidopsis floral meristem identity genes AP1, AGL24 and SVP directly repress class B and C floral homeotic genes.2009 · DOI: 10.1111/j.1365-313x.2009.03985.x
`At5g62165`	MADS-box transcription factor that acts with AGL71 and AGL72 in the control of flowering time.	The Arabidopsis SOC1-like genes AGL42, AGL71 and AGL72 promote flowering in the shoot apical and axillary meristems.2011 · DOI: 10.1111/j.1365-313x.2011.04653.x
`At4g22950`	Probable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner.	Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway.2006 · DOI: 10.1101/gad.377206
`At4g11880`	Transcriptional activator that regulates root development by controlling meristem size and patterning of the root apical meristem.	The MADS transcription factor XAL2/AGL14 modulates auxin transport during Arabidopsis root development by regulating PIN expression.2013 · DOI: 10.1038/emboj.2013.216

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0122600`	Probable transcription factor active in flowering time control.	Functional analyses of the flowering time gene OsMADS50, the putative SUPPRESSOR OF OVEREXPRESSION OF CO 1/AGAMOUS-LIKE 20 (SOC1/AGL20) ortholog in rice.2004 · DOI: 10.1111/j.1365-313x.2004.02082.x Reciprocal control of flowering time by OsSOC1 in transgenic Arabidopsis and by FLC in transgenic rice.2003 · DOI: 10.1046/j.1467-7652.2003.00034.x

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026790 · 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:0009409 response to cold Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0009838 abscission Biological Process

GO:0009908 flower development Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0009911 positive regulation of flower development Biological Process

GO:0010048 vernalization response Biological Process

GO:0010076 maintenance of floral meristem identity Biological Process

GO:0010077 maintenance of inflorescence meristem identity Biological Process

GO:0010082 regulation of root meristem growth Biological Process

KEGG gene cross-reference

ath:AT2G45660

ath:AT4G11880

ath:AT4G22950

ath:AT5G62165

dosa:Os03g0122600

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.

Nucleus0.966

Rank 1 · LXL04_026790 · OH-1004

Cytoplasm0.094

Rank 2 · LXL04_026790 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_026790 · OH-1004

Endoplasmic reticulum0.012

Rank 4 · LXL04_026790 · OH-1004

Plastid0.011

Rank 5 · LXL04_026790 · 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-TF10-57 aa

PF01486.23K-box84-171 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026790	`PF00319.24`	SRF-TF	10	57	2.5e-27	94.8
LXL04_026790	`PF01486.23`	K-box	84	171	1.7e-23	83.3

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
`O64645`	Arabidopsis thaliana	MADS-box protein SOC1	62.441%	Swiss-Prot	strong database homology
`Q9FIS1`	Arabidopsis thaliana	MADS-box protein AGL42	55.769%	Swiss-Prot	strong database homology
`O82743`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL19	55.963%	Swiss-Prot	strong database homology
`Q38838`	Arabidopsis thaliana	Agamous-like MADS-box protein AGL14	55.349%	Swiss-Prot	strong database homology
`Q9XJ60`	Oryza sativa subsp. japonica	MADS-box transcription factor 50	55.189%	Swiss-Prot	strong database homology

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