LXL04_000385 | RubberDandelionOmics

Gene overview

LXL04_000385

Reference: OH-1004 Chr: Chr01 Coordinates: 7154952-7158129 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2019 bp · LXL04_000385|LXL04_000385|OH1004|cDNA

ATGGCGAAGATGCAAGAAGAAGCTCTTCTCAAAATCTGCGATAAAAATATGAGCCAATTGAGTATCGAAACTGGAGATTCTTTTGCTACTTTACTCGAACTTGCTGCAAATAATGACATCGAGGGGTTCACCCAATCAATCGAGTCCGACTCATCTGGGATTGACGAGGTCGGATTATGGTATGGCCGTCAAAAGGGGTCAAAACAGATGGTTCTCGAACACAGAACTCCATTAATGGTAGCCGCCATGTATGGAAGCAT...

CDS

Download CDS FASTA

2019 bp · LXL04_000385|LXL04_000385|OH1004|CDS

ATGGCGAAGATGCAAGAAGAAGCTCTTCTCAAAATCTGCGATAAAAATATGAGCCAATTGAGTATCGAAACTGGAGATTCTTTTGCTACTTTACTCGAACTTGCTGCAAATAATGACATCGAGGGGTTCACCCAATCAATCGAGTCCGACTCATCTGGGATTGACGAGGTCGGATTATGGTATGGCCGTCAAAAGGGGTCAAAACAGATGGTTCTCGAACACAGAACTCCATTAATGGTAGCCGCCATGTATGGAAGCAT...

Protein

Download Protein FASTA

672 aa · LXL04_000385|LXL04_000385|OH1004|PROTEIN

MAKMQEEALLKICDKNMSQLSIETGDSFATLLELAANNDIEGFTQSIESDSSGIDEVGLWYGRQKGSKQMVLEHRTPLMVAAMYGSIDVLKLILSQSKVDVNRLCGVDKTTALHCAASGGSINAVEAIKLLLLNGADPNLIDVNGLRPVDMIVVSPKLPDMKKTLEELLGADGDLELPILNSLSPENHSPENRSPVSDPDLLSSPKISPFDTKREYPVDPSLPDIKNSIYSTDEFRMYSFKVRPCSRAYSHDWTECPFVH...

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_000385`
TK1151 ID	TkA01G615220
OH-1004 ID	LXL04_000385
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 100.000 / OH-1004 97.619 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_000385

Location Chr01:7154952-7158129 (+)

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_000385 · 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.

Cytoplasm0.666

Rank 1 · LXL04_000385 · OH-1004

Nucleus0.352

Rank 2 · LXL04_000385 · OH-1004

Cell membrane0.071

Rank 3 · LXL04_000385 · OH-1004

Lysosome / Vacuole0.039

Rank 4 · LXL04_000385 · OH-1004

Mitochondrion0.038

Rank 5 · LXL04_000385 · 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_270-142 aa

PF13606.13Ank_374-102 aa

PF00023.37Ank75-102 aa

PF13637.13Ank_478-126 aa

PF00023.37Ank110-142 aa

PF25512.2zf-CCCH_AtC3H23234-267 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000385	`PF12796.14`	Ank_2	70	142	4.9e-11	43.8
LXL04_000385	`PF13606.13`	Ank_3	74	102	9.6e-10	38.5
LXL04_000385	`PF00023.37`	Ank	75	102	3.4e-13	49.7
LXL04_000385	`PF13637.13`	Ank_4	78	126	1.3e-10	41.9
LXL04_000385	`PF00023.37`	Ank	110	142	3.4e-13	49.7
LXL04_000385	`PF25512.2`	zf-CCCH_AtC3H23	234	267	4.3e-22	78.2

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	60.876%	Swiss-Prot	strong database homology
`Q9LXV4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 56	50.281%	Swiss-Prot	strong database homology
`Q9LUZ4`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 66	44.038%	Swiss-Prot	moderate database homology
`Q10EL1`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 24	56.101%	Swiss-Prot	strong database homology
`Q2QPW2`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 67	45.322%	Swiss-Prot	moderate database homology

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