LXL04_013728 | RubberDandelionOmics

Gene overview

LXL04_013728

Reference: OH-1004 Chr: Chr03 Coordinates: 34899003-34901004 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1590 bp · LXL04_013728|LXL04_013728|OH1004|cDNA

ATGACCACTGATTTGGACAACTCGTCGGCCGTGAATGAGTCCACGGTATCTGGCGAAGCTAGTATTTCTTCTCCGGGCAATCAGACGGCGGGTCCTTCAGAAAAGCCAGCGAAAAGGAAGCGAAATTTAGCCGGCATGCCAGATCCAGATGCAGAGGTGATAGCTCTATCTCCAACAACATTAATGGCTACAAACCGTTTCGTATGTGAAATTTGCAGCAAGGGGTTTCAAAGAGACCAGAATCTGCAACTCCATAGAAG...

CDS

Download CDS FASTA

1590 bp · LXL04_013728|LXL04_013728|OH1004|CDS

ATGACCACTGATTTGGACAACTCGTCGGCCGTGAATGAGTCCACGGTATCTGGCGAAGCTAGTATTTCTTCTCCGGGCAATCAGACGGCGGGTCCTTCAGAAAAGCCAGCGAAAAGGAAGCGAAATTTAGCCGGCATGCCAGATCCAGATGCAGAGGTGATAGCTCTATCTCCAACAACATTAATGGCTACAAACCGTTTCGTATGTGAAATTTGCAGCAAGGGGTTTCAAAGAGACCAGAATCTGCAACTCCATAGAAG...

Protein

Download Protein FASTA

529 aa · LXL04_013728|LXL04_013728|OH1004|PROTEIN

MTTDLDNSSAVNESTVSGEASISSPGNQTAGPSEKPAKRKRNLAGMPDPDAEVIALSPTTLMATNRFVCEICSKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKRVYVCPEPSCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDQCSKKYAVQSDYKAHLKICGTREYKCDCGTLFSRRDSFITHRAFCDALAVETAKSQPEDESPKKDQQPKPQSVESTPQSTSTASPPPPPPPTITTTATIAPPVTSSVLCIVKSP...

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_013728`
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_013728

Location Chr03:34899003-34901004 (+)

Description Similar to ENY: Zinc finger protein ENHYDROUS

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g66730`	Transcription factor promoting the transition to germination by regulating light and hormonal signaling during seed maturation.	The Arabidopsis C2H2 zinc finger INDETERMINATE DOMAIN1/ENHYDROUS promotes the transition to germination by regulating light and hormonal signaling during seed maturation.2011 · DOI: 10.1105/tpc.111.085134 DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis.2014 · DOI: 10.1105/tpc.114.125690
`At1g03840`	Transcription factor that regulates tissue boundaries and asymmetric cell division.	DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins.2014 · DOI: 10.1073/pnas.1321669111
`At5g44160`	Transcription activator that binds to the DNA sequence 5'-CTTTTGTCC-3'.	Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in Arabidopsis.2011 · DOI: 10.1111/j.1365-313x.2010.04432.x AKIN10 delays flowering by inactivating IDD8 transcription factor through protein phosphorylation in Arabidopsis.2015 · DOI: 10.1186/s12870-015-0503-8
`At3g13810`	Probable transcription factor.	No verified direct reference in this release
`At3g45260`	Transcription factor that, together with JKD, regulates tissue boundaries and asymmetric cell division in roots by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action.	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_013728 · 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:0008356 asymmetric cell division Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009937 regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0009939 positive regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0010029 regulation of seed germination Biological Process

GO:0010075 regulation of meristem growth Biological Process

GO:0010150 leaf senescence Biological Process

GO:0010431 seed maturation Biological Process

GO:0034504 protein localization to nucleus Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

KEGG gene cross-reference

ath:AT1G03840

ath:AT3G13810

ath:AT3G45260

ath:AT5G44160

ath:AT5G66730

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.

Nucleus0.964

Rank 1 · LXL04_013728 · OH-1004

Cytoplasm0.143

Rank 2 · LXL04_013728 · OH-1004

Mitochondrion0.018

Rank 3 · LXL04_013728 · OH-1004

Cell membrane0.016

Rank 4 · LXL04_013728 · OH-1004

Endoplasmic reticulum0.007

Rank 5 · LXL04_013728 · 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.

PF22996.3C2H2-2nd_BIRD-IDD104-138 aa

PF22995.3C2CH-3rd_BIRD-IDD142-166 aa

PF22992.3C2CH-4th_BIRD-IDD169-205 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013728	`PF22996.3`	C2H2-2nd_BIRD-IDD	104	138	6.6e-23	81.2
LXL04_013728	`PF22995.3`	C2CH-3rd_BIRD-IDD	142	166	9.8e-15	54.7
LXL04_013728	`PF22992.3`	C2CH-4th_BIRD-IDD	169	205	1.4e-23	83.1

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
`Q9LVQ7`	Arabidopsis thaliana	Zinc finger protein ENHYDROUS	53.971%	Swiss-Prot	strong database homology
`Q9ZWA6`	Arabidopsis thaliana	Zinc finger protein MAGPIE	85.976%	Swiss-Prot	weak database homology
`Q9FFH3`	Arabidopsis thaliana	Zinc finger protein NUTCRACKER	85.366%	Swiss-Prot	weak database homology
`Q9LRW7`	Arabidopsis thaliana	Protein indeterminate-domain 11	83.529%	Swiss-Prot	weak database homology
`Q944L3`	Arabidopsis thaliana	Zinc finger protein BALDIBIS	82.424%	Swiss-Prot	weak database homology

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