LXL04_036273 | RubberDandelionOmics

Gene overview

LXL04_036273

Reference: OH-1004 Chr: Chr08 Coordinates: 39144902-39147118 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1911 bp · LXL04_036273|LXL04_036273|OH1004|cDNA

ATGGTATTCACGAAGCTTGTTCTTAGTTGCTACAACAAAAGAGTACCGCCTTTGAAGCGTGCAGTACAACATCTGTGTTATTCACATCTTCTATGGTTTCTGTCACTCTCTCGTTGTGAGTTTATTAGGGGTTTCTTTCAGAACGCCTCATTGTTAGTAGATAAGAGTCGCCATTTTCAAGCTACAAGTAATATATCCGACCTAAAGATGAACAAATTGACCGTCGAGACTGACGACACTTTTGCGACGTTACTCGAACT...

CDS

Download CDS FASTA

1911 bp · LXL04_036273|LXL04_036273|OH1004|CDS

ATGGTATTCACGAAGCTTGTTCTTAGTTGCTACAACAAAAGAGTACCGCCTTTGAAGCGTGCAGTACAACATCTGTGTTATTCACATCTTCTATGGTTTCTGTCACTCTCTCGTTGTGAGTTTATTAGGGGTTTCTTTCAGAACGCCTCATTGTTAGTAGATAAGAGTCGCCATTTTCAAGCTACAAGTAATATATCCGACCTAAAGATGAACAAATTGACCGTCGAGACTGACGACACTTTTGCGACGTTACTCGAACT...

Protein

Download Protein FASTA

636 aa · LXL04_036273|LXL04_036273|OH1004|PROTEIN

MVFTKLVLSCYNKRVPPLKRAVQHLCYSHLLWFLSLSRCEFIRGFFQNASLLVDKSRHFQATSNISDLKMNKLTVETDDTFATLLELAANNDLNGFKNLIEQDPSSIDEVGLWYGRQKGSKQMVLEHRTPLMVASMYGSIDVLKLILSLSKSDVNRSTGVDKTTALHCAAAGGSPNSVDVIKLLLSEGADPNLIDVNGLRPVDMIVVSPKFQNTKNALEELLETDKDAVLKTDFVSSPQIDGKREYPVDPSLPDIKNGIY...

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_036273`
TK1151 ID	TkA04G058600
OH-1004 ID	LXL04_036273
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.200
Protein coverage (%)	TK1151 98.722 / OH-1004 99.528 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_036273

Location Chr08:39144902-39147118 (+)

Description Similar to At2g41900: Zinc finger CCCH domain-containing protein 30

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g41900`	Zinc finger CCCH domain-containing protein 30.	No verified direct reference in this release
`At5g12850`	Zinc finger CCCH domain-containing protein 56.	No verified direct reference in this release
`At5g58620`	Zinc finger CCCH domain-containing protein 66.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0698800`	Zinc finger CCCH domain-containing protein 24.	No verified direct reference in this release
`Os12g0515500`	Zinc finger CCCH domain-containing protein 67.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_036273 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006412 translation Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0080090 regulation of primary metabolic process Biological Process

GO:1902074 response to salt Biological Process

GO:0000932 P-body Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT2G41900

ath:AT5G12850

ath:AT5G58620

dosa:Os03g0698800

dosa:Os12g0515500

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.

Cytoplasm0.582

Rank 1 · LXL04_036273 · OH-1004

Nucleus0.347

Rank 2 · LXL04_036273 · OH-1004

Cell membrane0.069

Rank 3 · LXL04_036273 · OH-1004

Mitochondrion0.062

Rank 4 · LXL04_036273 · OH-1004

Golgi apparatus0.062

Rank 5 · LXL04_036273 · 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.

PF12796.14Ank_288-195 aa

PF13637.13Ank_4131-185 aa

PF00023.37Ank163-195 aa

PF25512.2zf-CCCH_AtC3H23264-297 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036273	`PF12796.14`	Ank_2	88	195	1.8e-11	45.2
LXL04_036273	`PF13637.13`	Ank_4	131	185	2.9e-08	34.5
LXL04_036273	`PF00023.37`	Ank	163	195	1.1e-13	51.3
LXL04_036273	`PF25512.2`	zf-CCCH_AtC3H23	264	297	3.2e-21	75.5

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
`P93755`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 30	57.656%	Swiss-Prot	strong database homology
`Q9LXV4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 56	49.921%	Swiss-Prot	moderate database homology
`Q9LUZ4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 66	46.870%	Swiss-Prot	moderate database homology
`Q10EL1`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 24	55.178%	Swiss-Prot	strong database homology
`Q2QPW2`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 67	48.223%	Swiss-Prot	moderate database homology

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