LXL04_017631 | RubberDandelionOmics

Gene overview

LXL04_017631

Reference: OH-1004 Chr: Chr03 Coordinates: 155582718-155584945 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1521 bp · LXL04_017631|LXL04_017631|OH1004|cDNA

ATGGATTTCTCAGAATCTACAAAAATCGTATACGATAGGATCCAAAAACTAGAACCCGAAAAAGTCTCGAAGATTATCGGGTATCTCTTGTTACAAGATCATGGTGAAGAAGAGATGATACGATTAGCATATGGCCCCGATAATTTAATCCACTCGTTAATCAATAAAGCAAAAACCCACCTCAATTTACCCTCCAATTTCACTTCTCCGACACCAATTTCGAATTCTATAACGGATTTGCCCCTAAAGTTCGCACCTTT...

CDS

Download CDS FASTA

1521 bp · LXL04_017631|LXL04_017631|OH1004|CDS

ATGGATTTCTCAGAATCTACAAAAATCGTATACGATAGGATCCAAAAACTAGAACCCGAAAAAGTCTCGAAGATTATCGGGTATCTCTTGTTACAAGATCATGGTGAAGAAGAGATGATACGATTAGCATATGGCCCCGATAATTTAATCCACTCGTTAATCAATAAAGCAAAAACCCACCTCAATTTACCCTCCAATTTCACTTCTCCGACACCAATTTCGAATTCTATAACGGATTTGCCCCTAAAGTTCGCACCTTT...

Protein

Download Protein FASTA

506 aa · LXL04_017631|LXL04_017631|OH1004|PROTEIN

MDFSESTKIVYDRIQKLEPEKVSKIIGYLLLQDHGEEEMIRLAYGPDNLIHSLINKAKTHLNLPSNFTSPTPISNSITDLPLKFAPFSRNPQSLTSYPPSFPEDYHFQNQLHFLQLDNQIDPSNGSNYYSAPTLCPRISQRSPNLPESPIKICHYFLKGCCRHGNNCRYSHGIPANEPFSIFAPEDDNVFSPGSLQKLEIELTELLKSRKGYPVSIAALPLLYYEKFGKTLQAEGYLTESQRHGKAGYSLTKLLARLKRI...

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_017631`
TK1151 ID	TkA02G020350
OH-1004 ID	LXL04_017631
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
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_017631

Location Chr03:155582718-155584945 (+)

Description Similar to At2g05160: Zinc finger CCCH domain-containing protein 18

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g05160`	Possesses ribonuclease activity in vitro.	No verified direct reference in this release
`At3g51950`	Possesses RNA-binding and ribonuclease activities in vitro.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0126700`	Zinc finger CCCH domain-containing protein 54.	No verified direct reference in this release
`Os07g0583300`	Putative zinc finger CCCH domain-containing protein 51.	No verified direct reference in this release
`Os07g0682400`	Zinc finger CCCH domain-containing protein 53.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017631 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0004518 nuclease activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0016787 hydrolase activity Molecular Function

KEGG gene cross-reference

ath:AT2G05160

ath:AT3G51950

dosa:Os08g0126700

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.

Cytoplasm0.573

Rank 1 · LXL04_017631 · OH-1004

Nucleus0.435

Rank 2 · LXL04_017631 · OH-1004

Cell membrane0.065

Rank 3 · LXL04_017631 · OH-1004

Mitochondrion0.043

Rank 4 · LXL04_017631 · OH-1004

Endoplasmic reticulum0.041

Rank 5 · LXL04_017631 · 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.

PF23182.2PABC_AtC3H461-66 aa

PF16131.12Torus151-178 aa

PF00076.29RRM_1309-358 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017631	`PF23182.2`	PABC_AtC3H46	1	66	4e-35	120.6
LXL04_017631	`PF16131.12`	Torus	151	178	3e-07	31.7
LXL04_017631	`PF00076.29`	RRM_1	309	358	7.2e-07	29.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9SJ41`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 18	47.706%	Swiss-Prot	moderate database homology
`Q9SV09`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 46	38.500%	Swiss-Prot	moderate database homology
`Q6ZK57`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 54	44.282%	Swiss-Prot	moderate database homology
`Q84ZT0`	Oryza sativa subsp. japonica	Putative zinc finger CCCH domain-containing protein 51	48.684%	Swiss-Prot	weak database homology
`Q0D3J9`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 53	41.102%	Swiss-Prot	weak database homology

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