LXL04_027873 | RubberDandelionOmics

Gene overview

LXL04_027873

Reference: OH-1004 Chr: Chr06 Coordinates: 25340258-25341727 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

990 bp · LXL04_027873|LXL04_027873|OH1004|cDNA

ATGACTCCGATTTACTTAAACTCCATGTCTAATGATCAGTACAATGAACACCAATTCTTTAGCCCTGATCCACACATGGAGCACCAGTTCTTGAGCCCTAATTCTCAAGCTTCTTCGTCTTCCAACTCTCTCACCTGCCATCTTTTCTTCAACCCTAATGATCAAGATGCTCTTTTTGATAGAGAATCACATCCATCACAACTTGAGGGAGATAACTTCGGATCACAAGCATTCAATGATCTTCACATAGAGAATCGAGA...

CDS

Download CDS FASTA

990 bp · LXL04_027873|LXL04_027873|OH1004|CDS

ATGACTCCGATTTACTTAAACTCCATGTCTAATGATCAGTACAATGAACACCAATTCTTTAGCCCTGATCCACACATGGAGCACCAGTTCTTGAGCCCTAATTCTCAAGCTTCTTCGTCTTCCAACTCTCTCACCTGCCATCTTTTCTTCAACCCTAATGATCAAGATGCTCTTTTTGATAGAGAATCACATCCATCACAACTTGAGGGAGATAACTTCGGATCACAAGCATTCAATGATCTTCACATAGAGAATCGAGA...

Protein

Download Protein FASTA

329 aa · LXL04_027873|LXL04_027873|OH1004|PROTEIN

MTPIYLNSMSNDQYNEHQFFSPDPHMEHQFLSPNSQASSSSNSLTCHLFFNPNDQDALFDRESHPSQLEGDNFGSQAFNDLHIENRDDGDKNIGGLKFSLWKSETYDHMNDDNQVKWMSSKMRVMLKMKKSDPTKLNTLRSPSSTELKLDQDHQDHKELASSPLMEENANSNSFNSTSSNNNMAIPVRVCSDCNTTKTPLWRSGPRGPKSLCNACGIRQRKARKAMAMAETGKIAFDDDKPTSLKATKVLNKDHKKPNNG...

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_027873`
TK1151 ID	TkA07G099330
OH-1004 ID	LXL04_027873
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_027873

Location Chr06:25340258-25341727 (+)

Description Similar to GATA22: Putative GATA transcription factor 22

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g26150`	Transcriptional regulator that specifically binds 5'-GATA-3' or 5'-GAT-3' motifs within gene promoters.	The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS.2010 · DOI: 10.1101/gad.594910 Ectopic expression of different cytokinin-regulated transcription factor genes of Arabidopsis thaliana alters plant growth and development.2011 · DOI: 10.1016/j.jplph.2011.02.006 GNC and CGA1 modulate chlorophyll biosynthesis and glutamate synthase (GLU1/Fd-GOGAT) expression in Arabidopsis.2011 · DOI: 10.1371/journal.pone.0026765 Functional characterization of the GATA transcription factors GNC and CGA1 reveals their key role in chloroplast development, growth, and division in Arabidopsis.2012 · DOI: 10.1104/pp.112.198705 Cross-repressive interactions between SOC1 and the GATAs GNC and GNL/CGA1 in the control of greening, cold tolerance, and flowering time in Arabidopsis.2013 · DOI: 10.1104/pp.113.219238 Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana.2013 · DOI: 10.1073/pnas.1304250110
`At5g56860`	Transcriptional regulator that specifically binds 5'-GATA-3' or 5'-GAT-3' motifs within gene promoters.	No verified direct reference in this release
`At5g49300`	Transcriptional regulator that specifically binds 5'-GATA-3' or 5'-GAT-3' motifs within gene promoters.	No verified direct reference in this release
`At5g26930`	Transcriptional regulator that specifically binds 5'-GATA-3' or 5'-GAT-3' motifs within gene promoters.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0220400`	Transcriptional regulator that specifically binds 5'-GATA-3' or 5'-GAT-3' motifs within gene promoters (By similarity).	Rice cytokinin GATA transcription Factor1 regulates chloroplast development and plant architecture.2013 · DOI: 10.1104/pp.113.217265

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027873 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009646 response to absence of light Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009733 response to auxin Biological Process

GO:0009735 response to cytokinin Biological Process

GO:0009736 cytokinin-activated signaling pathway Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009909 regulation of flower development Biological Process

KEGG gene cross-reference

ath:AT4G26150

ath:AT5G26930

ath:AT5G49300

ath:AT5G56860

dosa:Os02g0220400

osa:4328751

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.

Nucleus0.964

Rank 1 · LXL04_027873 · OH-1004

Cytoplasm0.102

Rank 2 · LXL04_027873 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_027873 · OH-1004

Endoplasmic reticulum0.019

Rank 4 · LXL04_027873 · OH-1004

Plastid0.011

Rank 5 · LXL04_027873 · 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.

PF00320.34GATA190-224 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027873	`PF00320.34`	GATA	190	224	5.4e-17	61.8

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
`Q9SZI6`	Arabidopsis thaliana	Putative GATA transcription factor 22	38.793%	Swiss-Prot	moderate database homology
`Q5HZ36`	Arabidopsis thaliana	GATA transcription factor 21	43.750%	Swiss-Prot	weak database homology
`Q9FJ10`	Arabidopsis thaliana	GATA transcription factor 16	32.022%	Swiss-Prot	moderate database homology
`Q8LC59`	Arabidopsis thaliana	GATA transcription factor 23	71.795%	Swiss-Prot	weak database homology
`Q6YW48`	Oryza sativa subsp. japonica	Protein CYTOKININ-RESPONSIVE GATA TRANSCRIPTION FACTOR 1	43.810%	Swiss-Prot	weak database homology

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