LXL04_039155 | RubberDandelionOmics

Gene overview

LXL04_039155

Reference: OH-1004 Chr: Chr09 Coordinates: 60961991-60963637 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1458 bp · LXL04_039155|LXL04_039155|OH1004|cDNA

ATGAGTGGCAAACGCAGAAGGTTCAAGAATGATGACATCAGCAGAGGCAGAGATAGGAATATTCGGAGCTTTCATAATGACTGGGAAACACATTATACCACCACCACCCGCAAGCCATACAGGAGCAGGAGTAGAGGCAGAGAGTGGGAAACATATAACAAATCTTGTAGTAATGAATACAGTAGGCGTAGAGATGATGTAAGAAAAGAGTTTTATGGGGCCCGCGATCAATCCAATTCCAAATCCAGGCAAATTAGTAA...

CDS

Download CDS FASTA

1458 bp · LXL04_039155|LXL04_039155|OH1004|CDS

ATGAGTGGCAAACGCAGAAGGTTCAAGAATGATGACATCAGCAGAGGCAGAGATAGGAATATTCGGAGCTTTCATAATGACTGGGAAACACATTATACCACCACCACCCGCAAGCCATACAGGAGCAGGAGTAGAGGCAGAGAGTGGGAAACATATAACAAATCTTGTAGTAATGAATACAGTAGGCGTAGAGATGATGTAAGAAAAGAGTTTTATGGGGCCCGCGATCAATCCAATTCCAAATCCAGGCAAATTAGTAA...

Protein

Download Protein FASTA

485 aa · LXL04_039155|LXL04_039155|OH1004|PROTEIN

MSGKRRRFKNDDISRGRDRNIRSFHNDWETHYTTTTRKPYRSRSRGREWETYNKSCSNEYSRRRDDVRKEFYGARDQSNSKSRQISNIQCKFFAAGKCYRDDCRFSHHNPRSHDTWQPHDDDDDEEIHRSHNKPSWDWDDLDNKKRSWNGRPWDHDHDDNKTKSWNGNGTYSMDDKHRNDDNNNAHLNQNANVLDTSGKGQVEIEKSPKNDDDDVVGNLQGRKVAENEQDGNYEKSRSTRHKFTANNEYGRDDDDVRNNS...

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_039155`
TK1151 ID	TkA04G509820
OH-1004 ID	LXL04_039155
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	91.500
Protein coverage (%)	TK1151 94.831 / OH-1004 98.557 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_039155

Location Chr09:60961991-60963637 (+)

Description Similar to At3g18640: Zinc finger CCCH domain-containing protein 38

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g18640`	Zinc finger CCCH domain-containing protein 38.	No verified direct reference in this release
`At2g33835`	Transcriptional activator involved in the FRIGIDA-mediated vernalization pathway, but not in the autonomous flowering pathway.	FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana.2005 · DOI: 10.1242/dev.02170 The FRIGIDA complex activates transcription of FLC, a strong flowering repressor in Arabidopsis, by recruiting chromatin modification factors.2011 · DOI: 10.1105/tpc.110.075911

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0135800`	Zinc finger CCCH domain-containing protein 55.	No verified direct reference in this release
`Os05g0497500`	Zinc finger CCCH domain-containing protein 36.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_039155 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009908 flower development Biological Process

GO:0010220 positive regulation of vernalization response Biological Process

GO:0030154 cell differentiation Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G33835

ath:AT3G18640

dosa:Os05g0497500

dosa:Os08g0135800

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.

Nucleus0.948

Rank 1 · LXL04_039155 · OH-1004

Cytoplasm0.133

Rank 2 · LXL04_039155 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_039155 · OH-1004

Mitochondrion0.013

Rank 4 · LXL04_039155 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_039155 · 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.

PF23030.2SCAF11-like_C406-482 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039155	`PF23030.2`	SCAF11-like_C	406	482	1.4e-07	32.3

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
`Q9LIH5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 38	56.627%	Swiss-Prot	weak database homology
`Q84VG7`	Arabidopsis thaliana	Protein FRIGIDA-ESSENTIAL 1	45.679%	Swiss-Prot	weak database homology
`Q6YYC0`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 55	52.222%	Swiss-Prot	weak database homology
`Q75K81`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 36	54.667%	Swiss-Prot	weak database homology

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