LXL04_024638 | RubberDandelionOmics

Gene overview

LXL04_024638

Reference: OH-1004 Chr: Chr05 Coordinates: 95743466-95749630 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4029 bp · LXL04_024638|LXL04_024638|OH1004|cDNA

ATGATGGAGGGTCAAAATTTGGTAGCCGATAGTCAAATCTCTGATAGGGCTCAACCGATTGGCGATGGCTTAAAAGTGGTCGGTGGTGTGGTGGATGTTGTTCAGGCCGTCGCCGGTGGGGGAGTAAAGATGGAGTTAGGTAGCGGAGTAGGGGGAGGGGCAGCGTTGAAGAAGAAGCGAGGTAGGCCGCCTAAGGCTCAGGTGAAAGCGCCTCCTGCTAAGAAGAACAAAGAAgtggaggaagaagaagatgttTGCTT...

CDS

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4029 bp · LXL04_024638|LXL04_024638|OH1004|CDS

ATGATGGAGGGTCAAAATTTGGTAGCCGATAGTCAAATCTCTGATAGGGCTCAACCGATTGGCGATGGCTTAAAAGTGGTCGGTGGTGTGGTGGATGTTGTTCAGGCCGTCGCCGGTGGGGGAGTAAAGATGGAGTTAGGTAGCGGAGTAGGGGGAGGGGCAGCGTTGAAGAAGAAGCGAGGTAGGCCGCCTAAGGCTCAGGTGAAAGCGCCTCCTGCTAAGAAGAACAAAGAAGTGGAGGAAGAAGAAGATGTTTGCTT...

Protein

Download Protein FASTA

1342 aa · LXL04_024638|LXL04_024638|OH1004|PROTEIN

MMEGQNLVADSQISDRAQPIGDGLKVVGGVVDVVQAVAGGGVKMELGSGVGGGAALKKKRGRPPKAQVKAPPAKKNKEVEEEEDVCFICFDGGSLVLCDRRNCPKAYHPACIKRDEAFFESAAKWNCGWHICSMCEKPSHHMCYTCTYSLCRSCIRKSDYVCVRGDRGFCTICMKTIMLIENNGQGEDGKVQADFDDKLSWEYLFKVYWVYLKGKLSLTLDELTQAKNPWKIATTSTPITLSTIPSPLPSTTITPPPPPP...

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_024638`
TK1151 ID	TkA06G121840
OH-1004 ID	LXL04_024638
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.000
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_024638

Location Chr05:95743466-95749630 (-)

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

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Functional annotation source: OH1004 · LXL04_024638 · 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.

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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.

Nucleus0.958

Rank 1 · LXL04_024638 · OH-1004

Cytoplasm0.091

Rank 2 · LXL04_024638 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_024638 · OH-1004

Endoplasmic reticulum0.019

Rank 4 · LXL04_024638 · OH-1004

Plastid0.013

Rank 5 · LXL04_024638 · 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.

PF26291.1SWIB_eIF2D322-373 aa

PF02201.24SWIB328-393 aa

PF03126.24Plus-3460-560 aa

PF25980.1NERD_plant583-631 aa

PF02213.22GYF745-784 aa

PF18345.8zf_CCCH_41323-1341 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024638	`PF26291.1`	SWIB_eIF2D	322	373	7.9e-06	26.2
LXL04_024638	`PF02201.24`	SWIB	328	393	3.5e-15	56.2
LXL04_024638	`PF03126.24`	Plus-3	460	560	1.7e-20	74.3
LXL04_024638	`PF25980.1`	NERD_plant	583	631	2.2e-20	72.9
LXL04_024638	`PF02213.22`	GYF	745	784	5.8e-13	49.0
LXL04_024638	`PF18345.8`	zf_CCCH_4	1323	1341	8.9e-06	26.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SD34`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 44	43.890%	Swiss-Prot	moderate database homology
`Q9SIV5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 19	47.708%	Swiss-Prot	weak database homology
`Q9FT92`	Arabidopsis thaliana	Uncharacterized protein At5g08430	33.129%	Swiss-Prot	weak database homology

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