LXL04_011770 | RubberDandelionOmics

Gene overview

LXL04_011770

Reference: OH-1004 Chr: Chr02 Coordinates: 171453684-171456523 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1131 bp · LXL04_011770|LXL04_011770|OH1004|cDNA

ATGTCCAACTTCGTCGGAGAGGATCATGATGAGTGGTTCCACAGCAGTACTAGCCTCGTGCAATCATCATACGGAAGCCCAAACACTAATGACAATGGTGATGGCAGTTCTATCCCTCCGACGACCATGATCTCAAAGAAGAAACGAAATCTCCCTGGAAATCCAGGCAAGCTACACACAACCTTTTCATCAAATCCTGATGCTGAAGTTGTGGCCTTGTCTCCAAGGACTCTAATGGCTACAAATCGATATATATGTGA...

CDS

Download CDS FASTA

1131 bp · LXL04_011770|LXL04_011770|OH1004|CDS

ATGTCCAACTTCGTCGGAGAGGATCATGATGAGTGGTTCCACAGCAGTACTAGCCTCGTGCAATCATCATACGGAAGCCCAAACACTAATGACAATGGTGATGGCAGTTCTATCCCTCCGACGACCATGATCTCAAAGAAGAAACGAAATCTCCCTGGAAATCCAGGCAAGCTACACACAACCTTTTCATCAAATCCTGATGCTGAAGTTGTGGCCTTGTCTCCAAGGACTCTAATGGCTACAAATCGATATATATGTGA...

Protein

Download Protein FASTA

376 aa · LXL04_011770|LXL04_011770|OH1004|PROTEIN

MSNFVGEDHDEWFHSSTSLVQSSYGSPNTNDNGDGSSIPPTTMISKKKRNLPGNPGKLHTTFSSNPDAEVVALSPRTLMATNRYICEVCHKGFQRDQNLQLHRRGHNLPWKLKQRPANIQVKKRVYICPEPNCVHHEPTRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHAKICGTRQNNGIFLEINLFNTNTTCWLCRKDSFVTHRAFCDALTEESYKMDIKVGGIGGVLLIPEEMSGPLNISMRSSITS...

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_011770`
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_011770

Location Chr02:171453684-171456523 (-)

Description Similar to IDD12: Protein indeterminate-domain 12

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g02670`	Probable transcription factor.	No verified direct reference in this release
`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
`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
`At3g50700`	Transcription factor that acts as a positive regulator of gibberellin (GA) action, homeostasis and signaling.	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_011770 · 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:0010336 gibberellic acid homeostasis 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:AT3G45260

ath:AT3G50700

ath:AT4G02670

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.

Nucleus0.947

Rank 1 · LXL04_011770 · OH-1004

Cytoplasm0.130

Rank 2 · LXL04_011770 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_011770 · OH-1004

Mitochondrion0.013

Rank 4 · LXL04_011770 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_011770 · 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-IDD122-156 aa

PF22995.3C2CH-3rd_BIRD-IDD160-184 aa

PF22992.3C2CH-4th_BIRD-IDD208-230 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011770	`PF22996.3`	C2H2-2nd_BIRD-IDD	122	156	9.7e-22	77.4
LXL04_011770	`PF22995.3`	C2CH-3rd_BIRD-IDD	160	184	9e-15	54.8
LXL04_011770	`PF22992.3`	C2CH-4th_BIRD-IDD	208	230	1e-11	45.2

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
`O22759`	Arabidopsis thaliana	Protein indeterminate-domain 12	51.254%	Swiss-Prot	strong database homology
`Q9ZWA6`	Arabidopsis thaliana	Zinc finger protein MAGPIE	66.146%	Swiss-Prot	moderate database homology
`Q9LVQ7`	Arabidopsis thaliana	Zinc finger protein ENHYDROUS	66.486%	Swiss-Prot	weak database homology
`Q9SCQ6`	Arabidopsis thaliana	Zinc finger protein GAI-ASSOCIATED FACTOR 1	60.870%	Swiss-Prot	moderate database homology
`Q944L3`	Arabidopsis thaliana	Zinc finger protein BALDIBIS	68.108%	Swiss-Prot	weak database homology

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