LXL04_028033 | RubberDandelionOmics

Gene overview

LXL04_028033

Reference: OH-1004 Chr: Chr06 Coordinates: 29396162-29398066 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1236 bp · LXL04_028033|LXL04_028033|OH1004|cDNA

ATGGACGAAGAAGAATTACAGAAGCGATTCACTGATTGCGTCTATTTCTTAGCCTCTCCTCTCACTTGCAAGAAGGGAATTGAATGTGAATACCGGCATAGTGAGATTGCAAGGCTGAACCCTAGAGACTGCTGGTATTGGTTGGGAGGATGCTGTTTCAATCCCGATTGTGCTTTCAGACATCCTCCATTAGAAGGATTCAAGGAAGCATACCATGAACCTTCTAATCTCAACATCCCTCCTGCTTTACCTACAGACAA...

CDS

Download CDS FASTA

1236 bp · LXL04_028033|LXL04_028033|OH1004|CDS

ATGGACGAAGAAGAATTACAGAAGCGATTCACTGATTGCGTCTATTTCTTAGCCTCTCCTCTCACTTGCAAGAAGGGAATTGAATGTGAATACCGGCATAGTGAGATTGCAAGGCTGAACCCTAGAGACTGCTGGTATTGGTTGGGAGGATGCTGTTTCAATCCCGATTGTGCTTTCAGACATCCTCCATTAGAAGGATTCAAGGAAGCATACCATGAACCTTCTAATCTCAACATCCCTCCTGCTTTACCTACAGACAA...

Protein

Download Protein FASTA

411 aa · LXL04_028033|LXL04_028033|OH1004|PROTEIN

MDEEELQKRFTDCVYFLASPLTCKKGIECEYRHSEIARLNPRDCWYWLGGCCFNPDCAFRHPPLEGFKEAYHEPSNLNIPPALPTDKSHKSNIPCYFYSKGFCNKGDKCSFLHGHADVIPPLKPSKPTSMVNNIPLLSEKKSSAESQTGSPPVKPHPNPSEPTQIDHTDTIRKHTEDESQQEISTEEESQESESESGDVSNSVDLPEEFVQSESDVFNDQSPDFDLVFEERLGSDQDVDFFSDHQHEETEGDPIEYHHHH...

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_028033`
TK1151 ID	TkA07G114810
OH-1004 ID	LXL04_028033
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	91.900
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_028033

Location Chr06:29396162-29398066 (+)

Description Similar to Os02g0831100: Zinc finger CCCH domain-containing protein 19

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g02160`	Zinc finger CCCH domain-containing protein 17.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0831100`	Zinc finger CCCH domain-containing protein 19.	No verified direct reference in this release
`Os04g0671800`	Zinc finger CCCH domain-containing protein 32.	No verified direct reference in this release
`Os05g0176400`	Zinc finger CCCH domain-containing protein 34.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_028033 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006406 mRNA export from nucleus Biological Process

GO:0016973 poly(A)+ mRNA export from nucleus Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G02160

dosa:Os02g0831100

dosa:Os04g0671800

dosa:Os05g0176400

hsa:9877

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.

Nucleus0.906

Rank 1 · LXL04_028033 · OH-1004

Cytoplasm0.171

Rank 2 · LXL04_028033 · OH-1004

Cell membrane0.034

Rank 3 · LXL04_028033 · OH-1004

Endoplasmic reticulum0.020

Rank 4 · LXL04_028033 · OH-1004

Mitochondrion0.012

Rank 5 · LXL04_028033 · 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.

PF15663.12zf-CCCH_37-64 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028033	`PF15663.12`	zf-CCCH_3	7	64	4.4e-13	50.1

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
`Q9ZUM0`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 17	58.772%	Swiss-Prot	weak database homology
`Q6K977`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 19	53.279%	Swiss-Prot	weak database homology
`Q0J952`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 32	49.645%	Swiss-Prot	weak database homology
`Q6AT25`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 34	33.333%	Swiss-Prot	moderate database homology

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