LXL04_004686 | RubberDandelionOmics

Gene overview

LXL04_004686

Reference: OH-1004 Chr: Chr01 Coordinates: 143363562-143365203 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

894 bp · LXL04_004686|LXL04_004686|OH1004|cDNA

ATGTGCTTTGAAGCTCCACCGTTGTTTGAATGGCTCAAGCCATCTCCTCCTTCTACTTCATCGTCCTCTTCATATGACACCATGATGTTCTCTAAAGATCAAGAAACTATTCAGTGCTTACCCCTACTCAGTCGACTTATCAACCAAGATGAAAAAGATAGGGTTTTGAAGATCAAAGAAGAAGATCATAACATCGAGAAAGTGACAGTAACACTGCATATCGGATTGCCTAGTTATGCAGGAGATTCACCGGTCACTAA...

CDS

Download CDS FASTA

894 bp · LXL04_004686|LXL04_004686|OH1004|CDS

ATGTGCTTTGAAGCTCCACCGTTGTTTGAATGGCTCAAGCCATCTCCTCCTTCTACTTCATCGTCCTCTTCATATGACACCATGATGTTCTCTAAAGATCAAGAAACTATTCAGTGCTTACCCCTACTCAGTCGACTTATCAACCAAGATGAAAAAGATAGGGTTTTGAAGATCAAAGAAGAAGATCATAACATCGAGAAAGTGACAGTAACACTGCATATCGGATTGCCTAGTTATGCAGGAGATTCACCGGTCACTAA...

Protein

Download Protein FASTA

297 aa · LXL04_004686|LXL04_004686|OH1004|PROTEIN

MCFEAPPLFEWLKPSPPSTSSSSSYDTMMFSKDQETIQCLPLLSRLINQDEKDRVLKIKEEDHNIEKVTVTLHIGLPSYAGDSPVTNELFEEFKEEDEIKSDMKMVKLNNHHSDHDQTRFWIPTPSQILVGPMQFVCSLCNKTFNRYNNMQMHMWGHGSEYRKGPESLKGIQPAAMLRLPCYCCAQGCKNNINHPRAKPLKDFRTLQTHYKRKHGDKPFTCRKYCTKRFAVKGDWRTHEKNCGKLWYCTCGSDFKHKRSL...

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_004686`
TK1151 ID	TkA01G124810
OH-1004 ID	LXL04_004686
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_004686

Location Chr01:143363562-143365203 (-)

Description Similar to WIP3: Zinc finger protein WIP3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g08290`	Probable transcriptional regulator.	No verified direct reference in this release
`At3g20880`	Probable transcriptional regulator.	No verified direct reference in this release
`At1g51220`	Probable transcriptional regulator.	No verified direct reference in this release
`At3g57670`	Transcriptional regulator required for normal differentiation of the ovary transmitting tract cells and pollen tube growth.	No verified direct reference in this release
`At1g13290`	Probable transcriptional regulator (Probable).	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_004686 · 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: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

GO:0080022 primary root development Biological Process

KEGG gene cross-reference

ath:AT1G08290

ath:AT1G13290

ath:AT1G51220

ath:AT3G20880

ath:AT3G57670

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.

Nucleus0.978

Rank 1 · LXL04_004686 · OH-1004

Cytoplasm0.077

Rank 2 · LXL04_004686 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_004686 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_004686 · OH-1004

Plastid0.010

Rank 5 · LXL04_004686 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF23115.2zf-C2H2_STOP2_3rd181-215 aa

PF22995.3C2CH-3rd_BIRD-IDD218-243 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004686	`PF23115.2`	zf-C2H2_STOP2_3rd	181	215	4.7e-19	68.8
LXL04_004686	`PF22995.3`	C2CH-3rd_BIRD-IDD	218	243	5e-10	39.6

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
`Q9SGD1`	Arabidopsis thaliana	Zinc finger protein WIP3	55.457%	Swiss-Prot	strong database homology
`Q8W030`	Arabidopsis thaliana	Zinc finger protein WIP4	61.667%	Swiss-Prot	strong database homology
`Q8W031`	Arabidopsis thaliana	Zinc finger protein WIP5	55.596%	Swiss-Prot	strong database homology
`Q9SVY1`	Arabidopsis thaliana	Zinc finger protein WIP2	59.289%	Swiss-Prot	strong database homology
`Q9FX68`	Arabidopsis thaliana	Zinc finger protein WIP6	63.761%	Swiss-Prot	strong database homology

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