LXL04_007241 | RubberDandelionOmics

Gene overview

LXL04_007241

Reference: OH-1004 Chr: Chr02 Coordinates: 40877543-40883173 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3300 bp · LXL04_007241|LXL04_007241|OH1004|cDNA

ATGGAAGTTCGGAATTCGGAAGCTGAGAGTCATAGCTCTGACCAGAGTCAACCGATTCAGGAAACGGAAGGTGATGAGGGGTCGAAGGTGGTGGCTGGAGGTATGGTCGATGTTGATGAAGGTGGGGGAGTGGAGGTTGAGATAGGTAATGGAGGCGAGGGAGCTGAATTGGTGAAGAAGAAGCGTGGCCGGCCGCCTAGGGCTCAGGCGAAATCGCCGCCTATTAAGATAATTAAAGAAGAGGACGAGGATGTTTGCTT...

CDS

Download CDS FASTA

3300 bp · LXL04_007241|LXL04_007241|OH1004|CDS

ATGGAAGTTCGGAATTCGGAAGCTGAGAGTCATAGCTCTGACCAGAGTCAACCGATTCAGGAAACGGAAGGTGATGAGGGGTCGAAGGTGGTGGCTGGAGGTATGGTCGATGTTGATGAAGGTGGGGGAGTGGAGGTTGAGATAGGTAATGGAGGCGAGGGAGCTGAATTGGTGAAGAAGAAGCGTGGCCGGCCGCCTAGGGCTCAGGCGAAATCGCCGCCTATTAAGATAATTAAAGAAGAGGACGAGGATGTTTGCTT...

Protein

Download Protein FASTA

1099 aa · LXL04_007241|LXL04_007241|OH1004|PROTEIN

MEVRNSEAESHSSDQSQPIQETEGDEGSKVVAGGMVDVDEGGGVEVEIGNGGEGAELVKKKRGRPPRAQAKSPPIKIIKEEDEDVCFICFDGGSLVLCDRRGCPKAYHPACVKRDEAFFQSKAKWNCGWHICSICQKSAHHMCYTCTYSLCKGCIKKADYVCVRGDKGFCIVCMKTIMLIENNGQGKDEKGQVDFDDKTSWEYLFKVYWLYLKRKLSLTLDELTEATNPWKVVSTSTITSTSTTTPPSVTPSTCIQNGDK...

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_007241`
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_007241

Location Chr02:40877543-40883173 (-)

Description Similar to At3g51120: Zinc finger CCCH domain-containing protein 44

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g51120`	Zinc finger CCCH domain-containing protein 44.	No verified direct reference in this release
`UniProt: Q9SIV5`	Plays a central role in integrating RNA silencing and chromatin signals in 21 nt siRNA-dependent DNA methylation on cytosine pathway leading to transcriptional gene silencing of specific sequences.	No verified direct reference in this release
`At5g08430`	Uncharacterized protein At5g08430.	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_007241 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016593 Cdc73/Paf1 complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0042393 histone binding Molecular Function

GO:1990269 RNA polymerase II C-terminal domain phosphoserine binding Molecular Function

KEGG gene cross-reference

ath:AT2G16485

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.

Nucleus0.947

Rank 1 · LXL04_007241 · OH-1004

Cytoplasm0.106

Rank 2 · LXL04_007241 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_007241 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_007241 · OH-1004

Plastid0.013

Rank 5 · LXL04_007241 · 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.

PF13771.13zf-HC5HC2H76-122 aa

PF02201.24SWIB311-369 aa

PF03126.24Plus-3434-537 aa

PF25980.1NERD_plant560-598 aa

PF02213.22GYF721-761 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007241	`PF13771.13`	zf-HC5HC2H	76	122	1e-05	26.3
LXL04_007241	`PF02201.24`	SWIB	311	369	2.8e-14	53.3
LXL04_007241	`PF03126.24`	Plus-3	434	537	1e-20	75.0
LXL04_007241	`PF25980.1`	NERD_plant	560	598	1.1e-07	32.2
LXL04_007241	`PF02213.22`	GYF	721	761	1.3e-12	48.0

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
`Q9SD34`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 44	48.298%	Swiss-Prot	moderate database homology
`Q9SIV5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 19	48.318%	Swiss-Prot	moderate database homology
`Q9FT92`	Arabidopsis thaliana	Uncharacterized protein At5g08430	26.325%	Swiss-Prot	weak database homology

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