LXL04_037999 | RubberDandelionOmics

Gene overview

LXL04_037999

Reference: OH-1004 Chr: Chr09 Coordinates: 27945776-27948151 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1650 bp · LXL04_037999|LXL04_037999|OH1004|cDNA

ATGGACTTTTCAGAATCTACGAAAATCGTATATGATAGGATCCAAAAAATCGATCCTGAAAATGTCTCCAAGATTGTTGGATACCTTCTTCTACAAGATCATGGTGAAAGAGAAATGATAAGATTAGCATATTGCCCCGATAACTTAATCCACTCTTTAATCAAAAAAGCAAAATCCCACCTCAATTTACTACCCAATTCCAAAATCCCCGAAATGCCCCTACACTTCACACCATTCACACCTTCAACCCCTACCACCCG...

CDS

Download CDS FASTA

1650 bp · LXL04_037999|LXL04_037999|OH1004|CDS

ATGGACTTTTCAGAATCTACGAAAATCGTATATGATAGGATCCAAAAAATCGATCCTGAAAATGTCTCCAAGATTGTTGGATACCTTCTTCTACAAGATCATGGTGAAAGAGAAATGATAAGATTAGCATATTGCCCCGATAACTTAATCCACTCTTTAATCAAAAAAGCAAAATCCCACCTCAATTTACTACCCAATTCCAAAATCCCCGAAATGCCCCTACACTTCACACCATTCACACCTTCAACCCCTACCACCCG...

Protein

Download Protein FASTA

549 aa · LXL04_037999|LXL04_037999|OH1004|PROTEIN

MDFSESTKIVYDRIQKIDPENVSKIVGYLLLQDHGEREMIRLAYCPDNLIHSLIKKAKSHLNLLPNSKIPEMPLHFTPFTPSTPTTRHSPLTIQIPSQPVDYLPMVNYPASFPEDYNLLHNHNRLRFLDDPFDSVNSVNSPDFSLGHIRANRRSPSLPEFPFKVCHYFIKGFCRHGNNCRYLHPTSELTFNYFEDETVFSPGSLEKLELELTELLKARKGFPLSIASLPMMYYEKFGKSLQAEGYLTESQRHGKAGYSLT...

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_037999`
TK1151 ID	TkA04G373630
OH-1004 ID	LXL04_037999
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.200
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_037999

Location Chr09:27945776-27948151 (+)

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
`Os03g0328900`	Zinc finger CCCH domain-containing protein 22.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_037999 · 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.

Cytoplasm0.580

Rank 1 · LXL04_037999 · OH-1004

Nucleus0.437

Rank 2 · LXL04_037999 · OH-1004

Cell membrane0.059

Rank 3 · LXL04_037999 · OH-1004

Mitochondrion0.052

Rank 4 · LXL04_037999 · OH-1004

Endoplasmic reticulum0.035

Rank 5 · LXL04_037999 · 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

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037999	`PF23182.2`	PABC_AtC3H46	1	66	1.2e-34	119.1

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
`Q9SJ41`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 18	46.907%	Swiss-Prot	moderate database homology
`Q9SV09`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 46	34.298%	Swiss-Prot	moderate database homology
`Q6ZK57`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 54	45.455%	Swiss-Prot	moderate database homology
`Q84ZT0`	Oryza sativa subsp. japonica	Putative zinc finger CCCH domain-containing protein 51	45.455%	Swiss-Prot	weak database homology
`Q10M00`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 22	29.888%	Swiss-Prot	weak database homology

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