LXL04_004425 | RubberDandelionOmics

Gene overview

LXL04_004425

Reference: OH-1004 Chr: Chr01 Coordinates: 135508611-135511628 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1035 bp · LXL04_004425|LXL04_004425|OH1004|cDNA

ATGAGTAATGATGATCACCAGCAGCCTTACTTCAAATACTACGATGGATCATGGTTCAATCTGAATAAACCCTATCTGTCGTCTTCATCGTCATCTTCTTCACATCCCCCGCTTTCATTTTCTCATTATTCTCATAATTATCAGCCTTCACCTCCTTCTCCACCTCTCAGAGAAGctcttcctcttctttctttAACCCCAACTAACGATCATCAACAAAACCCTAAAAATGTTTCAGGTACTTCAAACTCCATGGAAAT...

CDS

Download CDS FASTA

1035 bp · LXL04_004425|LXL04_004425|OH1004|CDS

ATGAGTAATGATGATCACCAGCAGCCTTACTTCAAATACTACGATGGATCATGGTTCAATCTGAATAAACCCTATCTGTCGTCTTCATCGTCATCTTCTTCACATCCCCCGCTTTCATTTTCTCATTATTCTCATAATTATCAGCCTTCACCTCCTTCTCCACCTCTCAGAGAAGCTCTTCCTCTTCTTTCTTTAACCCCAACTAACGATCATCAACAAAACCCTAAAAATGTTTCAGGTACTTCAAACTCCATGGAAAT...

Protein

Download Protein FASTA

344 aa · LXL04_004425|LXL04_004425|OH1004|PROTEIN

MSNDDHQQPYFKYYDGSWFNLNKPYLSSSSSSSSHPPLSFSHYSHNYQPSPPSPPLREALPLLSLTPTNDHQQNPKNVSGTSNSMEIDPNNYKVFEDDETVTVALHLGLPNPSFCEADLISRLSNNDDVDDQKEVGEEEEDDEGTNYSNEYLSSTLNKGQYWIPTPSQILTGPTQFSCPLCFKTFNRYNNMQMHMWGHGSQYRRGPESLRGIQPTAMLRLPCYCCAPRCHNNIDHPRAKPLKDFRTLQTHYKRKHGIKPF...

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_004425`
TK1151 ID	TkA01G151190
OH-1004 ID	LXL04_004425
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.500
Protein coverage (%)	TK1151 92.558 / OH-1004 57.849 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_004425

Location Chr01:135508611-135511628 (+)

Description Similar to WIP2: Zinc finger protein WIP2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g57670`	Transcriptional regulator required for normal differentiation of the ovary transmitting tract cells and pollen tube growth.	No verified direct reference in this release
`At1g51220`	Probable transcriptional regulator.	No verified direct reference in this release
`At3g20880`	Probable transcriptional regulator.	No verified direct reference in this release
`At1g13290`	Probable transcriptional regulator (Probable).	No verified direct reference in this release
`At1g34790`	May act as a transcriptional regulator involved in the differentiation of young endothelium.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004425 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001709 cell fate determination Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009813 flavonoid biosynthetic process Biological Process

GO:0009860 pollen tube growth Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010500 transmitting tissue development Biological Process

GO:0010588 cotyledon vascular tissue pattern formation Biological Process

GO:0048364 root development Biological Process

GO:0048367 shoot system development Biological Process

KEGG gene cross-reference

ath:AT1G13290

ath:AT1G34790

ath:AT1G51220

ath:AT3G20880

ath:AT3G57670

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.

Nucleus0.975

Rank 1 · LXL04_004425 · OH-1004

Cytoplasm0.086

Rank 2 · LXL04_004425 · OH-1004

Cell membrane0.025

Rank 3 · LXL04_004425 · OH-1004

Endoplasmic reticulum0.017

Rank 4 · LXL04_004425 · OH-1004

Plastid0.012

Rank 5 · LXL04_004425 · 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.

PF23115.2zf-C2H2_STOP2_3rd222-256 aa

PF22995.3C2CH-3rd_BIRD-IDD259-283 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004425	`PF23115.2`	zf-C2H2_STOP2_3rd	222	256	6.3e-16	58.8
LXL04_004425	`PF22995.3`	C2CH-3rd_BIRD-IDD	259	283	2.2e-12	47.2

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
`Q9SVY1`	Arabidopsis thaliana	Zinc finger protein WIP2	61.830%	Swiss-Prot	strong database homology
`Q8W031`	Arabidopsis thaliana	Zinc finger protein WIP5	64.413%	Swiss-Prot	strong database homology
`Q8W030`	Arabidopsis thaliana	Zinc finger protein WIP4	62.013%	Swiss-Prot	strong database homology
`Q9FX68`	Arabidopsis thaliana	Zinc finger protein WIP6	60.246%	Swiss-Prot	moderate database homology
`Q8VWG3`	Arabidopsis thaliana	Protein TRANSPARENT TESTA 1	63.679%	Swiss-Prot	moderate database homology

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