LXL04_010419 | RubberDandelionOmics

Gene overview

LXL04_010419

Reference: OH-1004 Chr: Chr02 Coordinates: 146330375-146331641 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

837 bp · LXL04_010419|LXL04_010419|OH1004|cDNA

ATGAACTTCGGAGGCCAGAAGAGGGGCAGGCCGGATGGTGGTCGAAATGGAGCTCCCAAGCGACCAAAACAAGAAATGGATACACCTGGTGTAGGAAGCAAATCAAAGCCATGCATGAAGTTTTTCAGTACTTCCGGGTGCCAATTTGGTGAAGGCTGCCACTTCTTACACTATGTCCCAGGCGGCTACAATGCCGCCAACCAGTTCCCAAACATGGGCGGCAGAAAGCCCTCAATGCCGCCACCACAACCCTTCACCGC...

CDS

Download CDS FASTA

837 bp · LXL04_010419|LXL04_010419|OH1004|CDS

ATGAACTTCGGAGGCCAGAAGAGGGGCAGGCCGGATGGTGGTCGAAATGGAGCTCCCAAGCGACCAAAACAAGAAATGGATACACCTGGTGTAGGAAGCAAATCAAAGCCATGCATGAAGTTTTTCAGTACTTCCGGGTGCCAATTTGGTGAAGGCTGCCACTTCTTACACTATGTCCCAGGCGGCTACAATGCCGCCAACCAGTTCCCAAACATGGGCGGCAGAAAGCCCTCAATGCCGCCACCACAACCCTTCACCGC...

Protein

Download Protein FASTA

278 aa · LXL04_010419|LXL04_010419|OH1004|PROTEIN

MNFGGQKRGRPDGGRNGAPKRPKQEMDTPGVGSKSKPCMKFFSTSGCQFGEGCHFLHYVPGGYNAANQFPNMGGRKPSMPPPQPFTAGPPPPVKTKLCNKLNTPEGCTFGNKCRFAHSQAEIGGRPYENHHAPPPQMGYGGGYRPTPPGLAGNFGESATAKVSIDASLAGAVIGKGGVNAKHICQLTGVKLNISDHESDINQKNVELEGSFDQIKQASAMVSEVLMSLTGGGNPAKKGGGGGGGNNFKTKMCENFAKGKC...

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_010419`
TK1151 ID	TkA03G526680
OH-1004 ID	LXL04_010419
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	61.300
Protein coverage (%)	TK1151 72.222 / OH-1004 47.842 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_010419

Location Chr02:146330375-146331641 (+)

Description Similar to Os02g0194200: Zinc finger CCCH domain-containing protein 14

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g12130`	Zinc finger CCCH domain-containing protein 36.	No verified direct reference in this release
`At5g06770`	Zinc finger CCCH domain-containing protein 52.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0194200`	Zinc finger CCCH domain-containing protein 14.	No verified direct reference in this release
`Os06g0618100`	Zinc finger CCCH domain-containing protein 44.	No verified direct reference in this release
`Os04g0665700`	Zinc finger CCCH domain-containing protein 31.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010419 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0051252 regulation of RNA metabolic process Biological Process

GO:1900057 positive regulation of leaf senescence Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G12130

ath:AT5G06770

dosa:Os02g0194200

dosa:Os04g0665700

dosa:Os06g0618100

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.

Nucleus0.767

Rank 1 · LXL04_010419 · OH-1004

Cytoplasm0.466

Rank 2 · LXL04_010419 · OH-1004

Endoplasmic reticulum0.038

Rank 3 · LXL04_010419 · OH-1004

Cell membrane0.034

Rank 4 · LXL04_010419 · OH-1004

Mitochondrion0.030

Rank 5 · LXL04_010419 · 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.

PF25585.2zf-CCCH_DUS3L94-117 aa

PF18044.8zf-CCCH_4100-117 aa

PF00013.36KH_1159-222 aa

PF00642.31zf-CCCH247-272 aa

PF18044.8zf-CCCH_4250-270 aa

PF18345.8zf_CCCH_4252-270 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010419	`PF25585.2`	zf-CCCH_DUS3L	94	117	2.1e-11	44.3
LXL04_010419	`PF18044.8`	zf-CCCH_4	100	117	2.9e-11	43.6
LXL04_010419	`PF00013.36`	KH_1	159	222	1.2e-12	48.1
LXL04_010419	`PF00642.31`	zf-CCCH	247	272	9.5e-14	51.6
LXL04_010419	`PF18044.8`	zf-CCCH_4	250	270	2.9e-11	43.6
LXL04_010419	`PF18345.8`	zf_CCCH_4	252	270	6.9e-09	36.2

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
`Q9C7C3`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 36	47.241%	Swiss-Prot	moderate database homology
`Q9FG30`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 52	44.776%	Swiss-Prot	moderate database homology
`Q7F8R0`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 14	53.947%	Swiss-Prot	strong database homology
`Q69XQ3`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 44	54.639%	Swiss-Prot	strong database homology
`Q7XPK1`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 31	50.165%	Swiss-Prot	strong database homology

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