LXL04_003109 | RubberDandelionOmics

Gene overview

LXL04_003109

Reference: OH-1004 Chr: Chr01 Coordinates: 68010006-68011358 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

741 bp · LXL04_003109|LXL04_003109|OH1004|cDNA

ATGGACGGAAGTCAACCCTACAACCCTCGAACTGTTGAAGAGGTTTTCAGAGATTTTAAGAGTCGAAGAGCTGGCATCATCAAAGCCCTTACTACTGACGTCGAAGAGTTTTATCAGCAGTGCGACCCTgAAAAGGAAAACCTATGTCTGTACGGATTCCCGAATGAGCAGTGGGAGGTGAATCTGCCCGCGGAAGAGGTCCCACCGGAGCTTCCGGAACCTGCCCTGGGCATCAACTTTGCAAGAGACGGCATGCCCGA...

CDS

Download CDS FASTA

741 bp · LXL04_003109|LXL04_003109|OH1004|CDS

ATGGACGGAAGTCAACCCTACAACCCTCGAACTGTTGAAGAGGTTTTCAGAGATTTTAAGAGTCGAAGAGCTGGCATCATCAAAGCCCTTACTACTGACGTCGAAGAGTTTTATCAGCAGTGCGACCCTGAAAAGGAAAACCTATGTCTGTACGGATTCCCGAATGAGCAGTGGGAGGTGAATCTGCCCGCGGAAGAGGTCCCACCGGAGCTTCCGGAACCTGCCCTGGGCATCAACTTTGCAAGAGACGGCATGCCCGA...

Protein

Download Protein FASTA

246 aa · LXL04_003109|LXL04_003109|OH1004|PROTEIN

MDGSQPYNPRTVEEVFRDFKSRRAGIIKALTTDVEEFYQQCDPEKENLCLYGFPNEQWEVNLPAEEVPPELPEPALGINFARDGMPEKDWLALVAVHGDAWLLAVAFYFGARFGFDKADRKRLFNMINDLPTIFEVVSKKQVKDKSSVSNHSSSKSKSNSKAKGSELKFPKPKEDEDEGLDDEEEEEHGDTLCGSCGENYASDEFWICCDICEKWFHGSCVKITPARAEHIKQYKCPACTNKRARP

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_003109`
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_003109

Location Chr01:68010006-68011358 (+)

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

Arabidopsis / Rice Reference Genes and Papers

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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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0887700`	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: A2WXR5`	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
`Os02g0564100`	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_003109 · 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:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003712 transcription coregulator activity Molecular Function

GO:0003714 transcription corepressor activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0042393 histone binding Molecular Function

KEGG gene cross-reference

ath:AT3G42790

ath:AT5G20510

dosa:Os01g0887700

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.

Nucleus0.831

Rank 1 · LXL04_003109 · OH-1004

Cytoplasm0.243

Rank 2 · LXL04_003109 · OH-1004

Cell membrane0.037

Rank 3 · LXL04_003109 · OH-1004

Mitochondrion0.035

Rank 4 · LXL04_003109 · OH-1004

Endoplasmic reticulum0.023

Rank 5 · LXL04_003109 · 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.

PF12165.14Alfin11-138 aa

PF00628.36PHD193-239 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003109	`PF12165.14`	Alfin	11	138	9.7e-69	229.8
LXL04_003109	`PF00628.36`	PHD	193	239	9.9e-09	35.8

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
`Q5XEM9`	Arabidopsis thaliana	PHD finger protein ALFIN-LIKE 5	71.206%	Swiss-Prot	strong database homology
`Q9M2B4`	Arabidopsis thaliana	PHD finger protein ALFIN-LIKE 3	73.171%	Swiss-Prot	strong database homology
`Q7F2Z1`	Oryza sativa subsp. japonica	PHD finger protein ALFIN-LIKE 6	70.281%	Swiss-Prot	strong database homology
`A2WXR5`	Oryza sativa subsp. indica	PHD finger protein ALFIN-LIKE 6	69.880%	Swiss-Prot	strong database homology
`Q6Z7F4`	Oryza sativa subsp. japonica	PHD finger protein ALFIN-LIKE 7	67.339%	Swiss-Prot	strong database homology

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