LXL04_024275 | RubberDandelionOmics

Gene overview

LXL04_024275

Reference: OH-1004 Chr: Chr05 Coordinates: 86317068-86318182 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

855 bp · LXL04_024275|LXL04_024275|OH1004|cDNA

ATGCCTCCATATTCATCAACCTCCTCCGCCGTCATGCGGTCACGACAGAAACCACAGAACTTTTACAGATTCATCCACTCCGACGATGTCAACCAAGTCATTATCAGAATCCCAAACAAGTTTATCAGAGAACATCGGAAGAATATCCTGTTAAACAACGTCTTAATAACTGTTTCAGATGAGAAGATTTGGTCTTTAGGTTGGATGATCTCCGGCGACGGCAAGCTCTGGCTCCAGAAGGGTTGGCCGGAATTCGCAGA...

CDS

Download CDS FASTA

855 bp · LXL04_024275|LXL04_024275|OH1004|CDS

ATGCCTCCATATTCATCAACCTCCTCCGCCGTCATGCGGTCACGACAGAAACCACAGAACTTTTACAGATTCATCCACTCCGACGATGTCAACCAAGTCATTATCAGAATCCCAAACAAGTTTATCAGAGAACATCGGAAGAATATCCTGTTAAACAACGTCTTAATAACTGTTTCAGATGAGAAGATTTGGTCTTTAGGTTGGATGATCTCCGGCGACGGCAAGCTCTGGCTCCAGAAGGGTTGGCCGGAATTCGCAGA...

Protein

Download Protein FASTA

284 aa · LXL04_024275|LXL04_024275|OH1004|PROTEIN

MPPYSSTSSAVMRSRQKPQNFYRFIHSDDVNQVIIRIPNKFIREHRKNILLNNVLITVSDEKIWSLGWMISGDGKLWLQKGWPEFAEHYCLKTGYLLIFNYLRKSVFRVCIFDRNSCEINYAPSNFLEIQEPATQDDESIAMSETEALDTPTIVQEIKASGKGNEYRRRKRAPGSAKSFKSDYPFYSVKIKASYVNWGLYIPLPFVRRYLLCGDEKCVDCALQLPDGRLWSPVKCRDYNNYGKLYGGNWNRFRDENHVGV...

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_024275`
TK1151 ID	TkA06G157420
OH-1004 ID	LXL04_024275
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
Protein coverage (%)	TK1151 82.686 / OH-1004 82.394 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_024275

Location Chr05:86317068-86318182 (-)

Description Similar to VRN1: B3 domain-containing transcription factor VRN1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g18990`	Essential protein.	Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control.2002 · DOI: 10.1126/science.1072147 The Arabidopsis B3 domain protein VERNALIZATION1 (VRN1) is involved in processes essential for development, with structural and mutational studies revealing its DNA-binding surface.2013 · DOI: 10.1074/jbc.m112.438572
`At1g49475`	B3 domain-containing protein At1g49475.	No verified direct reference in this release
`At4g01580`	B3 domain-containing protein At4g01580.	No verified direct reference in this release
`At1g49480`	Involved in the regulation of vernalization (By similarity).	Ca2+-dependent GTPase, extra-large G protein 2 (XLG2), promotes activation of DNA-binding protein related to vernalization 1 (RTV1), leading to activation of floral integrator genes and early flowering in Arabidopsis.2012 · DOI: 10.1074/jbc.m111.317412
`At4g31640`	B3 domain-containing protein REM5.	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_024275 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009409 response to cold Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010048 vernalization response Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G49475

ath:AT1G49480

ath:AT3G18990

ath:AT4G01580

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.

Nucleus0.959

Rank 1 · LXL04_024275 · OH-1004

Cytoplasm0.099

Rank 2 · LXL04_024275 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_024275 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_024275 · OH-1004

Mitochondrion0.008

Rank 5 · LXL04_024275 · 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.

PF02362.27B324-115 aa

PF02362.27B3192-283 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024275	`PF02362.27`	B3	24	115	1.8e-25	89.5
LXL04_024275	`PF02362.27`	B3	192	283	1.8e-25	89.5

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
`Q8L3W1`	Arabidopsis thaliana	B3 domain-containing transcription factor VRN1	37.037%	Swiss-Prot	weak database homology
`Q9XIB4`	Arabidopsis thaliana	B3 domain-containing protein At1g49475	32.117%	Swiss-Prot	weak database homology
`Q9ZSH7`	Arabidopsis thaliana	B3 domain-containing protein At4g01580	30.000%	Swiss-Prot	weak database homology
`Q9XIB5`	Arabidopsis thaliana	B3 domain-containing protein REM19	35.345%	Swiss-Prot	weak database homology
`Q9SB80`	Arabidopsis thaliana	B3 domain-containing protein REM5	25.397%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card