LXL04_009249 | RubberDandelionOmics

Gene overview

LXL04_009249

Reference: OH-1004 Chr: Chr02 Coordinates: 121323088-121325964 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

696 bp · LXL04_009249|LXL04_009249|OH1004|cDNA

ATGGCACCCGCTCCACCGTCTCCAAACTCTCAAAACGCAAAGACCTCAGCAAAGCTGACGCCGCCGTTCTCAAAGACTGCATCGGAAAAATTAAAGACGCCATGGGCCAGTGCCGCCATCACCGACGAGTACACCTGCATTGATGAATTTTCCGACATGAAAGTCAGTCCGGCGGTCAAGAAGAAGATCAGGAGTAGTATTGAGAAGATTACCGGCTATATGAAATCGATTCCTTCTCAACGACCAGCTCGCCAGCAAGT...

CDS

Download CDS FASTA

696 bp · LXL04_009249|LXL04_009249|OH1004|CDS

ATGGCACCCGCTCCACCGTCTCCAAACTCTCAAAACGCAAAGACCTCAGCAAAGCTGACGCCGCCGTTCTCAAAGACTGCATCGGAAAAATTAAAGACGCCATGGGCCAGTGCCGCCATCACCGACGAGTACACCTGCATTGATGAATTTTCCGACATGAAAGTCAGTCCGGCGGTCAAGAAGAAGATCAGGAGTAGTATTGAGAAGATTACCGGCTATATGAAATCGATTCCTTCTCAACGACCAGCTCGCCAGCAAGT...

Protein

Download Protein FASTA

231 aa · LXL04_009249|LXL04_009249|OH1004|PROTEIN

MAPAPPSPNSQNAKTSAKLTPPFSKTASEKLKTPWASAAITDEYTCIDEFSDMKVSPAVKKKIRSSIEKITGYMKSIPSQRPARQQVTTTPLGQSQRVHVPGEKKAGEGLEFEVYNQGMSKTELCNKWQETGACPYGDNLDYMEWIRMLKVLMCRALDGWSICCVSGGQEDEYRSRRITFCIGRFSRSIFCVSLIWVLEDEPVPDSGVEFVASSLKLGLEEELGSDEFELF

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_009249`
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_009249

Location Chr02:121323088-121325964 (-)

Description Similar to Os05g0576300: Zinc finger CCCH domain-containing protein 39

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g66810`	Functions probably as a transcriptional factor that activates genes involved in secondary cell wall biosynthesis.	AtC3H14, a plant-specific tandem CCCH zinc-finger protein, binds to its target mRNAs in a sequence-specific manner and affects cell elongation in Arabidopsis thaliana.2014 · DOI: 10.1111/tpj.12667 Arabidopsis C3H14 and C3H15 have overlapping roles in the regulation of secondary wall thickening and anther development.2015 · DOI: 10.1093/jxb/erv060
`At1g68200`	Functions probably as a transcriptional factor that activates genes involved in secondary cell wall biosynthesis.	The Arabidopsis CALLOSE DEFECTIVE MICROSPORE1 gene is required for male fertility through regulating callose metabolism during microsporogenesis.2014 · DOI: 10.1104/pp.113.233387 Arabidopsis C3H14 and C3H15 have overlapping roles in the regulation of secondary wall thickening and anther development.2015 · DOI: 10.1093/jxb/erv060 The CCCH zinc finger protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid signaling.2022 · DOI: 10.1093/plphys/kiac046

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0576300`	Zinc finger CCCH domain-containing protein 39.	No verified direct reference in this release
`Os01g0645000`	Zinc finger CCCH domain-containing protein 9.	No verified direct reference in this release
`Os03g0301500`	Putative zinc finger CCCH domain-containing protein 21.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_009249 · 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:0009742 brassinosteroid mediated signaling pathway Biological Process

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

GO:0051511 negative regulation of unidimensional cell growth Biological Process

GO:1901347 negative regulation of secondary cell wall biogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G66810

ath:AT1G68200

dosa:Os01g0645000

dosa:Os05g0576300

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.

Cytoplasm0.376

Rank 1 · LXL04_009249 · OH-1004

Nucleus0.313

Rank 2 · LXL04_009249 · OH-1004

Mitochondrion0.146

Rank 3 · LXL04_009249 · OH-1004

Cell membrane0.133

Rank 4 · LXL04_009249 · OH-1004

Endoplasmic reticulum0.121

Rank 5 · LXL04_009249 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00642.31zf-CCCH121-139 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009249	`PF00642.31`	zf-CCCH	121	139	1.4e-06	28.7

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
`Q9C9N3`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 14	48.052%	Swiss-Prot	weak database homology
`Q9C9F5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 15	54.412%	Swiss-Prot	weak database homology
`Q6L5G1`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 39	46.250%	Swiss-Prot	weak database homology
`A2ZVY5`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 9	31.707%	Swiss-Prot	moderate database homology
`Q10MN8`	Oryza sativa subsp. japonica	Putative zinc finger CCCH domain-containing protein 21	47.059%	Swiss-Prot	weak database homology

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