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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

TkA01G437930
Reference: TK1151 Chr: Chr01 Coordinates: 109440405-109445820 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2434 bp · TkA01G437930|TK1151|cDNA

TCAGAATTCAACAAAATTCGCAGAGATTTTAATTTTTTTTTTCTTTTTCTTTTTCCTCCCGTTCTCGTAGGAAAACCTGCCGATCTCCATAAACAAAAACCCTAATTCTCTCCCCCATCTTTCTCTCTCCTCGCACATTTTTCACAGGGAGAGTCACTTGAACATCATGGACACAGATGATAAATTTGTTGCTAAAGGTGTTCAAAGTCTATCTTCCAGTGTTCAAAGCACCCCAGAGAAAAACGGTCACTCAGATGATG...

CDS

Download CDS FASTA

1863 bp · TkA01G437930|TK1151|CDS

ATGGACACAGATGATAAATTTGTTGCTAAAGGTGTTCAAAGTCTATCTTCCAGTGTTCAAAGCACCCCAGAGAAAAACGGTCACTCAGATGATGCTTCAAGAACTCCCGATCCACTTCTCGTGAAATCCGACACCCGGAAAGATCTATTCGGTACTTGTTCCGAAAAGGGTAAAAAACAATCAGCTTCATCAAAACATAAAATGACCGAACCGTCCCTGAGGCTAAACAAAAAAACTTCAAAAAACCAAGATCCCAAAAA...

Protein

Download Protein FASTA

620 aa · TkA01G437930|TK1151|PROTEIN

MDTDDKFVAKGVQSLSSSVQSTPEKNGHSDDASRTPDPLLVKSDTRKDLFGTCSEKGKKQSASSKHKMTEPSLRLNKKTSKNQDPKKDSPSPKCQQSRKQNRKGENPIRIPPESHSDAKFPDTWICKNSACRAVLSVTDTFCKRCSCCICRLFDDNKDPSLWLECTSDSSNGESCGLSCHIECALLQKKVGVVNHGQLMQLDGSYCCASCGKVSGILGYWKKQLAIAKDARRVDSLCYRIYLSFRLLDGTSRFQELHEIV...

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 IDTkA01G437930
TK1151 IDTkA01G437930
OH-1004 IDLXL04_039343
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)36.700
Protein coverage (%)TK1151 84.194 / OH-1004 81.818
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 versionTK1151 / GWHBCHF00000000
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDTkA01G437930
LocationChr01:109440405-109445820 (-)
DescriptionSimilar to VIL2: VIN3-like protein 2
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
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
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

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. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

Nucleus0.960
Rank 1 · TkA01G437930 · TK1151
Cytoplasm0.090
Rank 2 · TkA01G437930 · TK1151
Cell membrane0.035
Rank 3 · TkA01G437930 · TK1151
Endoplasmic reticulum0.018
Rank 4 · TkA01G437930 · TK1151
Plastid0.014
Rank 5 · TkA01G437930 · TK1151

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.

PF07227PHD_Oberon126-244 aa
PF02259FAT232-304 aa
PF23376Fn3_VIN3332-418 aa
PF00041fn3332-412 aa
PF25059FN3_DSCAM-DSCAML_C354-408 aa
PF16656Pur_ac_phosph_N365-405 aa
PF16656Pur_ac_phosph_N489-516 aa
PF23380VIN3_C536-608 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA01G437930PF07227PHD_Oberon1262446.9e-33114.0
TkA01G437930PF02259FAT2323040.02614.5
TkA01G437930PF23376Fn3_VIN33324186.2e-2897.5
TkA01G437930PF00041fn33324123.1e-0524.8
TkA01G437930PF25059FN3_DSCAM-DSCAML_C3544080.113.7
TkA01G437930PF16656Pur_ac_phosph_N3654050.02116.1
TkA01G437930PF16656Pur_ac_phosph_N4895160.02116.1
TkA01G437930PF23380VIN3_C5366085.2e-39132.6
TkA01G437930PF07227PHD_Oberon5395556.9e-33114.0

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9LHF5Arabidopsis thalianasp|Q9LHF5|VIL1_ARATH VIN3-like protein 147.600%Swiss-ProtMedium
Q9SUM4Arabidopsis thalianasp|Q9SUM4|VIL2_ARATH VIN3-like protein 233.900%Swiss-ProtMedium
Q9FIE3Arabidopsis thalianasp|Q9FIE3|VIN3_ARATH Protein VERNALIZATION INSENSITIVE 336.500%Swiss-ProtMedium
Q5BPT4Arabidopsis thalianasp|Q5BPT4|VIL3_ARATH VIN3-like protein 335.800%Swiss-ProtMedium

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