LXL04_013012 | RubberDandelionOmics

Gene overview

LXL04_013012

Reference: OH-1004 Chr: Chr03 Coordinates: 22230438-22231979 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1542 bp · LXL04_013012|LXL04_013012|OH1004|cDNA

ATGTGTAGTGGTTCCGATCAGTTAACCTCCAGAACGCCATCTGCTTCCCTGTTCAAAGATATGAACGATTCGATAAAAATAATTCAACCCGACCCGTCTTTCTCCGATTTGCTCGAGTTTGCAGCTAATAACGACGTCGAAGGATTCAAGCAATTAATCGATCGAATTCCTTCCGCCATTAACGAAGTGGGAATCTGGTACGGCCGTCAAAGAAGCTCAAAACGTATGATAATGGAGCACAAAACTCCATTGATGATCGC...

CDS

Download CDS FASTA

1542 bp · LXL04_013012|LXL04_013012|OH1004|CDS

ATGTGTAGTGGTTCCGATCAGTTAACCTCCAGAACGCCATCTGCTTCCCTGTTCAAAGATATGAACGATTCGATAAAAATAATTCAACCCGACCCGTCTTTCTCCGATTTGCTCGAGTTTGCAGCTAATAACGACGTCGAAGGATTCAAGCAATTAATCGATCGAATTCCTTCCGCCATTAACGAAGTGGGAATCTGGTACGGCCGTCAAAGAAGCTCAAAACGTATGATAATGGAGCACAAAACTCCATTGATGATCGC...

Protein

Download Protein FASTA

513 aa · LXL04_013012|LXL04_013012|OH1004|PROTEIN

MCSGSDQLTSRTPSASLFKDMNDSIKIIQPDPSFSDLLEFAANNDVEGFKQLIDRIPSAINEVGIWYGRQRSSKRMIMEHKTPLMIAATYGSVDVVKLILSCTEVNVNSTCGPDKTTALHCAASGGSTNAFDVIKILLISGADADLVDADGRRPADVLLVPPNLPNLKISIVKLLKNGGFCAEQEDEIDLTSFKSIEKKEYPIDPFFPDLKSDGYSTDEFRMFAFKIRPCSRAYSHDWTECPFIHPGESARRRDPRKIHY...

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_013012`
TK1151 ID	TkA02G523160
OH-1004 ID	LXL04_013012
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013012

Location Chr03:22230438-22231979 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At2g40140`	Involved in salt stress response.	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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013012 · 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:0009409 response to cold Biological Process

GO:0009651 response to salt stress Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0071456 cellular response to hypoxia 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

KEGG gene cross-reference

ath:AT2G40140

ath:AT2G41900

ath:AT5G12850

ath:AT5G58620

dosa:Os03g0698800

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.550

Rank 1 · LXL04_013012 · OH-1004

Nucleus0.431

Rank 2 · LXL04_013012 · OH-1004

Cell membrane0.092

Rank 3 · LXL04_013012 · OH-1004

Mitochondrion0.049

Rank 4 · LXL04_013012 · OH-1004

Endoplasmic reticulum0.043

Rank 5 · LXL04_013012 · 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_241-147 aa

PF00023.37Ank81-109 aa

PF13637.13Ank_485-131 aa

PF00023.37Ank116-148 aa

PF25512.2zf-CCCH_AtC3H23219-252 aa

PF00642.31zf-CCCH263-284 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013012	`PF12796.14`	Ank_2	41	147	9.9e-12	46.0
LXL04_013012	`PF00023.37`	Ank	81	109	3e-12	46.7
LXL04_013012	`PF13637.13`	Ank_4	85	131	8.8e-08	33.0
LXL04_013012	`PF00023.37`	Ank	116	148	3e-12	46.7
LXL04_013012	`PF25512.2`	zf-CCCH_AtC3H23	219	252	2.2e-19	69.6
LXL04_013012	`PF00642.31`	zf-CCCH	263	284	3.1e-06	27.7

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
`P93755`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 30	52.165%	Swiss-Prot	strong database homology
`Q9LXV4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 56	50.410%	Swiss-Prot	strong database homology
`Q9LUZ4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 66	47.368%	Swiss-Prot	moderate database homology
`Q9XEE6`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 29	40.592%	Swiss-Prot	moderate database homology
`Q10EL1`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 24	51.852%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card