LXL04_027810 | RubberDandelionOmics

Gene overview

LXL04_027810

Reference: OH-1004 Chr: Chr06 Coordinates: 24349569-24350897 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

732 bp · LXL04_027810|LXL04_027810|OH1004|cDNA

ATGGATGCTGCCGGTGCCGCTGCGTACAATCCTCGGACCGTCGAAGAAGTCTTCAGAGATTACAAAGGCCGTCGAAATGGCATGATCAAAGCCCTCACAACCGATGTTGGAGATTTTTTCCGCCAGTGCGATCCTGAGAAGGAAAATCTCTGCTTATATGGATTCCCTAGCGAACAATGGGAGGTCAACTTACCTGCAGAAGAGGTCCCTCCAGAGCTTCCCGAGCCTGCACTAGGTATCAACTTTGCCAGAGATGGAAT...

CDS

Download CDS FASTA

732 bp · LXL04_027810|LXL04_027810|OH1004|CDS

ATGGATGCTGCCGGTGCCGCTGCGTACAATCCTCGGACCGTCGAAGAAGTCTTCAGAGATTACAAAGGCCGTCGAAATGGCATGATCAAAGCCCTCACAACCGATGTTGGAGATTTTTTCCGCCAGTGCGATCCTGAGAAGGAAAATCTCTGCTTATATGGATTCCCTAGCGAACAATGGGAGGTCAACTTACCTGCAGAAGAGGTCCCTCCAGAGCTTCCCGAGCCTGCACTAGGTATCAACTTTGCCAGAGATGGAAT...

Protein

Download Protein FASTA

243 aa · LXL04_027810|LXL04_027810|OH1004|PROTEIN

MDAAGAAAYNPRTVEEVFRDYKGRRNGMIKALTTDVGDFFRQCDPEKENLCLYGFPSEQWEVNLPAEEVPPELPEPALGINFARDGMQENDWLSLVAVHSDAWLLSVAFYFGARFGFDKSDRKRLFNMINDLPTIFEVVSGNSKKQTKMTNHSLHKSKSNTKGQGSESFQGKVNEEEEEDEEDEHGDALCGACGENYASDEFWICCDLCERWFHGKCVKITPAKAEHIKHYKCPSCSNKRARP

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_027810`
TK1151 ID	TkA07G095670
OH-1004 ID	LXL04_027810
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	89.500
Protein coverage (%)	TK1151 83.154 / OH-1004 98.354 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_027810

Location Chr06:24349569-24350897 (+)

Description Similar to AL5: PHD finger protein ALFIN-LIKE 5

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g20510`	Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.	No verified direct reference in this release
`At3g42790`	Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.	No verified direct reference in this release
`At2g02470`	Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0444900`	Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.	No verified direct reference in this release
`UniProt: A2XTW9`	Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027810 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0016036 cellular response to phosphate starvation Biological Process

GO:0030003 intracellular monoatomic cation homeostasis Biological Process

GO:0048767 root hair elongation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G02470

ath:AT3G42790

ath:AT5G20510

dosa:Os04g0444900

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.

Nucleus0.881

Rank 1 · LXL04_027810 · OH-1004

Cytoplasm0.186

Rank 2 · LXL04_027810 · OH-1004

Cell membrane0.036

Rank 3 · LXL04_027810 · OH-1004

Mitochondrion0.025

Rank 4 · LXL04_027810 · OH-1004

Endoplasmic reticulum0.022

Rank 5 · LXL04_027810 · 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.

PF12165.14Alfin13-140 aa

PF00628.36PHD190-236 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027810	`PF12165.14`	Alfin	13	140	3.5e-68	227.9
LXL04_027810	`PF00628.36`	PHD	190	236	4.2e-09	37.0

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
`Q5XEM9`	Arabidopsis thaliana	PHD finger protein ALFIN-LIKE 5	72.093%	Swiss-Prot	strong database homology
`Q9M2B4`	Arabidopsis thaliana	PHD finger protein ALFIN-LIKE 3	70.445%	Swiss-Prot	strong database homology
`Q8S8M9`	Arabidopsis thaliana	PHD finger protein ALFIN-LIKE 6	68.145%	Swiss-Prot	strong database homology
`Q7XUW3`	Oryza sativa subsp. japonica	PHD finger protein ALFIN-LIKE 4	61.382%	Swiss-Prot	strong database homology
`A2XTW9`	Oryza sativa subsp. indica	PHD finger protein ALFIN-LIKE 4	60.976%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card