LXL04_039143 | RubberDandelionOmics

Gene overview

LXL04_039143

Reference: OH-1004 Chr: Chr09 Coordinates: 60701548-60711452 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3303 bp · LXL04_039143|LXL04_039143|OH1004|cDNA

ATGTCCCATTTGTACTTGTACTTTGGTGGTGGAGAAAATGATATTGCTTGTGAGGTGGAGACTGAAACTTGGAATGCGATGTTTAAATGGATTGAGTTGGAACCAGGAAATATGGAAACGGTGAAAGGGTTGTTCTTGTGGACCGATAATCTTAACATGTCTTTGAAGAAAAGAGAGGTGATAGATGCAATTGCTTGTATTGGGATTACGACCGAAACTGAAGGTCGCTGGTGGACAAATTGGAAAGCGACGGTGCACAG...

CDS

Download CDS FASTA

3303 bp · LXL04_039143|LXL04_039143|OH1004|CDS

ATGTCCCATTTGTACTTGTACTTTGGTGGTGGAGAAAATGATATTGCTTGTGAGGTGGAGACTGAAACTTGGAATGCGATGTTTAAATGGATTGAGTTGGAACCAGGAAATATGGAAACGGTGAAAGGGTTGTTCTTGTGGACCGATAATCTTAACATGTCTTTGAAGAAAAGAGAGGTGATAGATGCAATTGCTTGTATTGGGATTACGACCGAAACTGAAGGTCGCTGGTGGACAAATTGGAAAGCGACGGTGCACAG...

Protein

Download Protein FASTA

1100 aa · LXL04_039143|LXL04_039143|OH1004|PROTEIN

MSHLYLYFGGGENDIACEVETETWNAMFKWIELEPGNMETVKGLFLWTDNLNMSLKKREVIDAIACIGITTETEGRWWTNWKATVHRRWGCKCGVEGVSLGTVNSRQRRQREGVSDGGTPSRRTGWSAGGTSKTYLSRTSEKRDDRRMEKLEGIRRRFLWGGDEDKRKIHWVAWEKVVTPKKKGGLGVGSIKAINIGLLVKWWWRLKTQPHSLWRKFIFGVHNLGKKPPDYLARKNMTGVWKNIAEMEKILMQIGVGFHD...

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_039143`
TK1151 ID	TkA04G508590
OH-1004 ID	LXL04_039143
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 47.545 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_039143

Location Chr09:60701548-60711452 (+)

Description Similar to VIL3: VIN3-like protein 3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g18880`	Involved in both the vernalization and photoperiod pathways by regulating gene expression.	No verified direct reference in this release
`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
`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
`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
`At1g65750`	Putative ribonuclease H protein At1g65750.	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_039143 · 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:0048587 regulation of short-day photoperiodism, flowering Biological Process

GO:0070417 cellular response to cold Biological Process

GO:0140719 constitutive heterochromatin formation Biological Process

KEGG gene cross-reference

ath:AT2G18880

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.

Nucleus0.691

Rank 1 · LXL04_039143 · OH-1004

Cytoplasm0.209

Rank 2 · LXL04_039143 · OH-1004

Cell membrane0.085

Rank 3 · LXL04_039143 · OH-1004

Endoplasmic reticulum0.043

Rank 4 · LXL04_039143 · OH-1004

Plastid0.042

Rank 5 · LXL04_039143 · 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_Oberon709-829 aa

PF23376.2Fn3_VIN3912-999 aa

PF23380.2VIN3_C1029-1098 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039143	`PF07227.18`	PHD_Oberon	709	829	1.7e-32	112.7
LXL04_039143	`PF23376.2`	Fn3_VIN3	912	999	2.7e-15	57.0
LXL04_039143	`PF23380.2`	VIN3_C	1029	1098	7.1e-31	106.5

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
`Q5BPT4`	Arabidopsis thaliana	VIN3-like protein 3	36.609%	Swiss-Prot	weak database homology
`Q9FIE3`	Arabidopsis thaliana	Protein VERNALIZATION INSENSITIVE 3	40.189%	Swiss-Prot	weak database homology
`Q9SUM4`	Arabidopsis thaliana	VIN3-like protein 2	37.634%	Swiss-Prot	weak database homology
`Q9LHF5`	Arabidopsis thaliana	VIN3-like protein 1	39.721%	Swiss-Prot	weak database homology
`P0C2F6`	Arabidopsis thaliana	Putative ribonuclease H protein At1g65750	35.398%	Swiss-Prot	weak database homology

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