LXL04_000708 | RubberDandelionOmics

Gene overview

LXL04_000708

Reference: OH-1004 Chr: Chr01 Coordinates: 12987116-12991620 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2433 bp · LXL04_000708|LXL04_000708|OH1004|cDNA

ATGTCGTCGCCGGCGAAGATTTGCATGAACGGATTGTGCGGGGCAACGACGACTCCTCAATGGAAGAAAGGTTGGCCCATGAAAACCGGCGGTTTTGCTAATCTCTGCTACGCTTGCGGAACTGCATATGATAATGTACGCTACTGTGAAAGGTTCCATCTTAATGAAGCAGGTTGGAGAGAATGCAATTCTTGTGAAAAGCCTGTTCATTGTGGATGCGTTGTTTCAAAATATCTTCATGAATGCCTTGATTTAGGAGG...

CDS

Download CDS FASTA

2433 bp · LXL04_000708|LXL04_000708|OH1004|CDS

ATGTCGTCGCCGGCGAAGATTTGCATGAACGGATTGTGCGGGGCAACGACGACTCCTCAATGGAAGAAAGGTTGGCCCATGAAAACCGGCGGTTTTGCTAATCTCTGCTACGCTTGCGGAACTGCATATGATAATGTACGCTACTGTGAAAGGTTCCATCTTAATGAAGCAGGTTGGAGAGAATGCAATTCTTGTGAAAAGCCTGTTCATTGTGGATGCGTTGTTTCAAAATATCTTCATGAATGCCTTGATTTAGGAGG...

Protein

Download Protein FASTA

810 aa · LXL04_000708|LXL04_000708|OH1004|PROTEIN

MSSPAKICMNGLCGATTTPQWKKGWPMKTGGFANLCYACGTAYDNVRYCERFHLNEAGWRECNSCEKPVHCGCVVSKYLHECLDLGGILCIKCIRANTTQSLNQTIVNEIPNGFARFSATWQQPSYFDKLLTPLTTQGSEKQQHQHQNTSSTSTISLQFKQDEKTPIPTPTPCSNKDITSTFLKPLPLPLPLPSIFQNQLPDKNQKPNLGLKPTYEPFNSSLLPTSNGVTIHEKVTVVKQEQKRGPKPSKSGIRSHANKG...

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_000708`
TK1151 ID	TkA01G592860
OH-1004 ID	LXL04_000708
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.000
Protein coverage (%)	TK1151 99.344 / OH-1004 96.543 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_000708

Location Chr01:12987116-12991620 (+)

Description Similar to VAL2: B3 domain-containing transcription repressor VAL2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g32010`	Transcriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3.	Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes.2007 · DOI: 10.1104/pp.106.092320
`At2g30470`	Transcriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3.	Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor.2005 · DOI: 10.1104/pp.104.057752 Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes.2007 · DOI: 10.1104/pp.106.092320 Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings.2007 · DOI: 10.1073/pnas.0607940104
`At4g21550`	May be involved in plant development.	Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes.2007 · DOI: 10.1104/pp.106.092320

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0563300`	B3 domain-containing protein Os07g0563300.	No verified direct reference in this release
`Os07g0679700`	B3 domain-containing protein Os07g0679700.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000708 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009744 response to sucrose Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G30470

ath:AT4G32010

dosa:Os07g0563300

dosa:Os07g0679700

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.973

Rank 1 · LXL04_000708 · OH-1004

Cytoplasm0.075

Rank 2 · LXL04_000708 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_000708 · OH-1004

Endoplasmic reticulum0.015

Rank 4 · LXL04_000708 · OH-1004

Plastid0.014

Rank 5 · LXL04_000708 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF25813.2zf_VAL1_N52-98 aa

PF02362.27B3312-411 aa

PF07496.22zf-CW523-565 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000708	`PF25813.2`	zf_VAL1_N	52	98	2.1e-21	76.3
LXL04_000708	`PF02362.27`	B3	312	411	2.8e-17	63.2
LXL04_000708	`PF07496.22`	zf-CW	523	565	7.5e-12	45.8

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
`Q5CCK4`	Arabidopsis thaliana	B3 domain-containing transcription repressor VAL2	42.643%	Swiss-Prot	moderate database homology
`Q8W4L5`	Arabidopsis thaliana	B3 domain-containing transcription repressor VAL1	43.609%	Swiss-Prot	moderate database homology
`O65420`	Arabidopsis thaliana	B3 domain-containing transcription factor VAL3	47.934%	Swiss-Prot	weak database homology
`Q0D5G4`	Oryza sativa subsp. japonica	B3 domain-containing protein Os07g0563300	46.995%	Swiss-Prot	moderate database homology
`Q6Z3U3`	Oryza sativa subsp. japonica	B3 domain-containing protein Os07g0679700	52.695%	Swiss-Prot	moderate database homology

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