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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_039343
Reference: OH-1004 Chr: JAJTUU010000010.1 Coordinates: 3577920-3581155 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1785 bp · LXL04_039343|LXL04_039343|OH1004|cDNA

ATGGATTCTTCCTCTTTCGAAGgGTTTGTGCTTGATCCATCATCAAATTGCAGTAAATTAAGCATGGAAGAAAAAAGAGAAATCGTATACGAAGTATCCGAATGGTCACACGGAGCACCCGAGCTCCTACAATCTTGGAGCCGTCAAGAAATTCTCCAAATCCTATGTTCCGAAATGGGAAAAGAACGAaagtacacgggtctcacaaaATTAAAAATCATCGAACATCTTCTCAAAATCGTATCcgaaaaaaaatcaaa...

CDS

Download CDS FASTA

1785 bp · LXL04_039343|LXL04_039343|OH1004|CDS

ATGGATTCTTCCTCTTTCGAAGGGTTTGTGCTTGATCCATCATCAAATTGCAGTAAATTAAGCATGGAAGAAAAAAGAGAAATCGTATACGAAGTATCCGAATGGTCACACGGAGCACCCGAGCTCCTACAATCTTGGAGCCGTCAAGAAATTCTCCAAATCCTATGTTCCGAAATGGGAAAAGAACGAAAGTACACGGGTCTCACAAAATTAAAAATCATCGAACATCTTCTCAAAATCGTATCCGAAAAAAAATCAAA...

Protein

Download Protein FASTA

594 aa · LXL04_039343|LXL04_039343|OH1004|PROTEIN

MDSSSFEGFVLDPSSNCSKLSMEEKREIVYEVSEWSHGAPELLQSWSRQEILQILCSEMGKERKYTGLTKLKIIEHLLKIVSEKKSNNLEYEHDMISNIESSENGGPTKRHRKSDHPNRLFNSTDNHNSSVNVVDLDVVEFCKNSACRAKLGEDGGFCKRCSCCICRSSDPPFLGGSCGMSCHLECALRHDKSGIVTKDRGLDGSFFCVSCGKMNDLLGCWRKQMMIARDTRRVDILCYRVSLSQKLLGGTIRYKKLAEV...

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.

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ID Mapping

Input IDLXL04_039343
Source versionOH-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 IDLXL04_039343
LocationJAJTUU010000010.1:3577920-3581155 (+)
DescriptionSimilar to VIL2: VIN3-like protein 2
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g30200 Maybe involved in both the vernalization and photoperiod pathways by regulating gene expression.
The Plant Homeo Domain finger protein, VIN3-LIKE 2, is necessary for photoperiod-mediated epigenetic regulation of the floral repressor, MAF5.2010 · DOI: 10.1073/pnas.1010834107
At5g57380 Plays a central role in vernalization by mediating the initial transcriptional repression of the homeotic gene FLC, a floral repressor, after a cold treatment.
Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3.2004 · DOI: 10.1038/nature02195
A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis.2006 · DOI: 10.1101/gad.1493306
The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis FLC.2007 · DOI: 10.1016/j.cub.2006.11.052
At2g18880 Involved in both the vernalization and photoperiod pathways by regulating gene expression. No verified direct reference in this release
At3g24440 Involved in both the vernalization and photoperiod pathways by regulating expression of the related floral repressors FLOWERING LOCUS C (FLC) and FLOWERING LOCUS M (FLM).
A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis.2006 · DOI: 10.1101/gad.1493306
The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis FLC.2007 · DOI: 10.1016/j.cub.2006.11.052
A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization.2008 · DOI: 10.1073/pnas.0808687105

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_039343 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0001666 response to hypoxia Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0009409 response to cold Biological Process
GO:0009908 flower development Biological Process
GO:0010048 vernalization response Biological Process
GO:0010228 vegetative to reproductive phase transition of meristem Biological Process
GO:0032922 circadian regulation of gene expression Biological Process
GO:0040029 epigenetic regulation of gene expression Biological Process
GO:0045814 negative regulation of gene expression, epigenetic Biological Process
GO:0048572 short-day photoperiodism Biological Process
GO:0048575 short-day photoperiodism, flowering Biological Process
GO:0048587 regulation of short-day photoperiodism, flowering Biological Process
KEGG gene cross-reference
ath:AT2G18880
ath:AT3G24440
ath:AT4G30200
ath:AT5G57380
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.

Nucleus0.942
Rank 1 · LXL04_039343 · OH-1004
Cytoplasm0.107
Rank 2 · LXL04_039343 · OH-1004
Cell membrane0.037
Rank 3 · LXL04_039343 · OH-1004
Endoplasmic reticulum0.021
Rank 4 · LXL04_039343 · OH-1004
Plastid0.015
Rank 5 · LXL04_039343 · 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.

PF07227.18PHD_Oberon142-246 aa
PF23376.2Fn3_VIN3330-415 aa
PF23380.2VIN3_C508-580 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_039343PF07227.18PHD_Oberon1422462.1e-2176.9
LXL04_039343PF23376.2Fn3_VIN33304157e-1555.7
LXL04_039343PF23380.2VIN3_C5085801.1e-35121.9

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9SUM4Arabidopsis thalianaVIN3-like protein 239.728%Swiss-Protmoderate database homology
Q9FIE3Arabidopsis thalianaProtein VERNALIZATION INSENSITIVE 338.594%Swiss-Protmoderate database homology
Q5BPT4Arabidopsis thalianaVIN3-like protein 332.504%Swiss-Protmoderate database homology
Q9LHF5Arabidopsis thalianaVIN3-like protein 134.528%Swiss-Protweak database homology

JBrowse

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