LXL04_003066 | RubberDandelionOmics

Gene overview

LXL04_003066

Reference: OH-1004 Chr: Chr01 Coordinates: 66407867-66408865 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

834 bp · LXL04_003066|LXL04_003066|OH1004|cDNA

ATGTTCACATCTACACCAATGCAACCATGTTCTTCAAAACATACAATTAAGGTGAAAGGCGAAGTACATGAAGTGGACAATGTTATTGATCTCTCTTCCTCTTCCTCTGACTCCTCAAAAAATGACGAAAATACCCCTTCATGTGCTGATTCCCAGAAACAATTGGTACTTTACAACAGTCCATGTAAGCCTCCATCATCTTTGCCAAGGGTATTACCGTCCGTAGGTGCATTCACTGTCCAATGTGCCAACTGTTTTAA...

CDS

Download CDS FASTA

834 bp · LXL04_003066|LXL04_003066|OH1004|CDS

ATGTTCACATCTACACCAATGCAACCATGTTCTTCAAAACATACAATTAAGGTGAAAGGCGAAGTACATGAAGTGGACAATGTTATTGATCTCTCTTCCTCTTCCTCTGACTCCTCAAAAAATGACGAAAATACCCCTTCATGTGCTGATTCCCAGAAACAATTGGTACTTTACAACAGTCCATGTAAGCCTCCATCATCTTTGCCAAGGGTATTACCGTCCGTAGGTGCATTCACTGTCCAATGTGCCAACTGTTTTAA...

Protein

Download Protein FASTA

277 aa · LXL04_003066|LXL04_003066|OH1004|PROTEIN

MFTSTPMQPCSSKHTIKVKGEVHEVDNVIDLSSSSSDSSKNDENTPSCADSQKQLVLYNSPCKPPSSLPRVLPSVGAFTVQCANCFKWRLIPTLEKYQEIRQHITEMPFVCETALEWRSDVSCDDPADIEQDGSRLWAIDKPNIAQPPPGWQRQLRIRGEGCLKFADVYYTAPTGKQLRSIPDVEKFLDKHPEYMEQGVTLSQFSFQTPKPLQENYVRKRPARVPDGIPEPMAALPGPHQHTDLQLDLRVYPLVKKARSA...

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_003066`
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_003066

Location Chr01:66407867-66408865 (-)

Description No functional description available

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g35330`	Probable transcriptional regulator.	No verified direct reference in this release
`At5g35338`	Probable transcriptional regulator.	No verified direct reference in this release
`At4g22745`	Probable transcriptional regulator.	No verified direct reference in this release
`At3g63030`	Transcriptional regulator that binds CpG, CpNpN and CpNpG (N is A, T, or C) islands in promoters regardless the DNA methylation status.	No verified direct reference in this release
`At4g00416`	Probable transcriptional regulator.	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_003066 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0000118 histone deacetylase complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016581 NuRD complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0008327 methyl-CpG binding Molecular Function

GO:0019899 enzyme binding Molecular Function

KEGG gene cross-reference

ath:AT3G63030

ath:AT4G00416

ath:AT4G22745

ath:AT5G35330

ath:AT5G35338

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.

Nucleus0.875

Rank 1 · LXL04_003066 · OH-1004

Cytoplasm0.199

Rank 2 · LXL04_003066 · OH-1004

Mitochondrion0.036

Rank 3 · LXL04_003066 · OH-1004

Cell membrane0.026

Rank 4 · LXL04_003066 · OH-1004

Endoplasmic reticulum0.015

Rank 5 · LXL04_003066 · 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.

PF07496.22zf-CW79-128 aa

PF01429.26MBD148-211 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003066	`PF07496.22`	zf-CW	79	128	7e-10	39.5
LXL04_003066	`PF01429.26`	MBD	148	211	1.5e-14	54.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8LA53`	Arabidopsis thaliana	Methyl-CpG-binding domain-containing protein 2	62.295%	Swiss-Prot	moderate database homology
`Q9FZP6`	Arabidopsis thaliana	Putative methyl-CpG-binding domain protein 12	49.650%	Swiss-Prot	moderate database homology
`Q5XEN5`	Arabidopsis thaliana	Methyl-CpG-binding domain-containing protein 1	38.065%	Swiss-Prot	moderate database homology
`Q9LYB9`	Arabidopsis thaliana	Methyl-CpG-binding domain-containing protein 4	37.857%	Swiss-Prot	moderate database homology
`Q4PSK1`	Arabidopsis thaliana	Methyl-CpG-binding domain-containing protein 3	32.117%	Swiss-Prot	weak database homology

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