LXL04_039343 | RubberDandelionOmics

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

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.

ID Mapping

Input ID	`LXL04_039343`
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_039343

Location JAJTUU010000010.1:3577920-3581155 (+)

Description Similar to VIL2: VIN3-like protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / 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 ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039343	`PF07227.18`	PHD_Oberon	142	246	2.1e-21	76.9
LXL04_039343	`PF23376.2`	Fn3_VIN3	330	415	7e-15	55.7
LXL04_039343	`PF23380.2`	VIN3_C	508	580	1.1e-35	121.9

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

Protein	Organism	Description	Identity	Database	Confidence
`Q9SUM4`	Arabidopsis thaliana	VIN3-like protein 2	39.728%	Swiss-Prot	moderate database homology
`Q9FIE3`	Arabidopsis thaliana	Protein VERNALIZATION INSENSITIVE 3	38.594%	Swiss-Prot	moderate database homology
`Q5BPT4`	Arabidopsis thaliana	VIN3-like protein 3	32.504%	Swiss-Prot	moderate database homology
`Q9LHF5`	Arabidopsis thaliana	VIN3-like protein 1	34.528%	Swiss-Prot	weak database homology

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