LXL04_009888 | RubberDandelionOmics

Gene overview

LXL04_009888

Reference: OH-1004 Chr: Chr02 Coordinates: 135399915-135402356 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1341 bp · LXL04_009888|LXL04_009888|OH1004|cDNA

ATGTTAGAAAAGCTTGTAGAAGATGAAGCCATAATCCCAAATGATCCTGAAGCTGAGGTTATCGCGTTGTCACCCAAGACTCTAATGGCAACAAACAGATTCTTGTGCGAGATTTGTGGAAAGGGATTCCAAAGAGATCAAAACCTTCAGCTCCATCGGCGAGGTCATAACCTGCCATGGAAACTAAAGCAAAGAACAAGCAAAGAAGTTAGAAAACGGGTTTACGTGTGCCCCGAGAAGTCGTGCGTCCATAACCATCC...

CDS

Download CDS FASTA

1341 bp · LXL04_009888|LXL04_009888|OH1004|CDS

ATGTTAGAAAAGCTTGTAGAAGATGAAGCCATAATCCCAAATGATCCTGAAGCTGAGGTTATCGCGTTGTCACCCAAGACTCTAATGGCAACAAACAGATTCTTGTGCGAGATTTGTGGAAAGGGATTCCAAAGAGATCAAAACCTTCAGCTCCATCGGCGAGGTCATAACCTGCCATGGAAACTAAAGCAAAGAACAAGCAAAGAAGTTAGAAAACGGGTTTACGTGTGCCCCGAGAAGTCGTGCGTCCATAACCATCC...

Protein

Download Protein FASTA

446 aa · LXL04_009888|LXL04_009888|OH1004|PROTEIN

MLEKLVEDEAIIPNDPEAEVIALSPKTLMATNRFLCEICGKGFQRDQNLQLHRRGHNLPWKLKQRTSKEVRKRVYVCPEKSCVHNHPSRALGDLTGIKKHFCRKHGEKKWKCAKCSKCYAVQSDWKAHSKTCGTREYKCDCGTLFSRRDSFITHRAFCDALAEETARVTAASNFNNVTTTAAGSLGNINYHFVGPPVLAGPTMVQHFSSIFKPISPNPQTHLDPTQQAGVLSLWESTGINDNNEEPNHHNNLQEIQQINS...

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_009888`
TK1151 ID	TkA03G480280
OH-1004 ID	LXL04_009888
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	91.100
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009888

Location Chr02:135399915-135402356 (+)

Description Similar to MGP: Zinc finger protein MAGPIE

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`At2g02080`	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable).	No verified direct reference in this release
`At3g50700`	Transcription factor that acts as a positive regulator of gibberellin (GA) action, homeostasis and signaling.	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_009888 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002221 pattern recognition receptor signaling pathway Biological Process

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:0010336 gibberellic acid homeostasis Biological Process

GO:0010431 seed maturation Biological Process

KEGG gene cross-reference

ath:AT1G03840

ath:AT2G02080

ath:AT3G50700

ath:AT5G44160

ath:AT5G66730

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.

Nucleus0.970

Rank 1 · LXL04_009888 · OH-1004

Cytoplasm0.114

Rank 2 · LXL04_009888 · OH-1004

Cell membrane0.020

Rank 3 · LXL04_009888 · OH-1004

Mitochondrion0.011

Rank 4 · LXL04_009888 · OH-1004

Endoplasmic reticulum0.009

Rank 5 · LXL04_009888 · 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-IDD71-105 aa

PF22995.3C2CH-3rd_BIRD-IDD109-133 aa

PF22992.3C2CH-4th_BIRD-IDD136-173 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009888	`PF22996.3`	C2H2-2nd_BIRD-IDD	71	105	5.7e-21	75.0
LXL04_009888	`PF22995.3`	C2CH-3rd_BIRD-IDD	109	133	1.7e-12	47.5
LXL04_009888	`PF22992.3`	C2CH-4th_BIRD-IDD	136	173	6e-24	84.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9ZWA6`	Arabidopsis thaliana	Zinc finger protein MAGPIE	52.147%	Swiss-Prot	strong database homology
`Q9FFH3`	Arabidopsis thaliana	Zinc finger protein NUTCRACKER	49.783%	Swiss-Prot	moderate database homology
`Q9LVQ7`	Arabidopsis thaliana	Zinc finger protein ENHYDROUS	49.606%	Swiss-Prot	moderate database homology
`Q8GYC1`	Arabidopsis thaliana	Protein indeterminate-domain 4, chloroplastic	41.907%	Swiss-Prot	moderate database homology
`Q9SCQ6`	Arabidopsis thaliana	Zinc finger protein GAI-ASSOCIATED FACTOR 1	88.235%	Swiss-Prot	weak database homology

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