LXL04_039773 | RubberDandelionOmics

Gene overview

LXL04_039773

Reference: OH-1004 Chr: JAJTUU010000039.1 Coordinates: 248257-250505 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

783 bp · LXL04_039773|LXL04_039773|OH1004|cDNA

ATGAAGATTCAGTGTAACGTATGTGAGATGGCGGAGGCGACGGTGCTTTGTTGCGCCGACGAGGCGGCTCTATGTTGGATTTGCGATGAGAAGGTACACGCTGCCAATAAGCTCGCCAGCAAGCATCAGAGAGTTCTTCTGTCAAATTCTAATTCTCAGATGCCTAAGTGTGATATTTGCCAGGAAACAGTTGGCTTCTTTTGTCTGGAAGATAGGGCATTACTGTGCAGAAAATGCGATGTTGCAATACATACAGCCAA...

CDS

Download CDS FASTA

783 bp · LXL04_039773|LXL04_039773|OH1004|CDS

ATGAAGATTCAGTGTAACGTATGTGAGATGGCGGAGGCGACGGTGCTTTGTTGCGCCGACGAGGCGGCTCTATGTTGGATTTGCGATGAGAAGGTACACGCTGCCAATAAGCTCGCCAGCAAGCATCAGAGAGTTCTTCTGTCAAATTCTAATTCTCAGATGCCTAAGTGTGATATTTGCCAGGAAACAGTTGGCTTCTTTTGTCTGGAAGATAGGGCATTACTGTGCAGAAAATGCGATGTTGCAATACATACAGCCAA...

Protein

Download Protein FASTA

260 aa · LXL04_039773|LXL04_039773|OH1004|PROTEIN

MKIQCNVCEMAEATVLCCADEAALCWICDEKVHAANKLASKHQRVLLSNSNSQMPKCDICQETVGFFCLEDRALLCRKCDVAIHTANTFVSSHQRFLLTGVKVGKEAAEHGASNITKTNVQSSPSDQYNKKLPPVQAAENDYFAPPSPPDGIQNWQFDKYLGILTDLNHNYNYIDNGPSKANGGKLGDSDCSAILGAMEAELDEGLGQVPEASWAVPQICSPPPTLTHNWPKNNDHPHHFEPPAFVPDICYSHVPDVYRF

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_039773`
TK1151 ID	TkA04G351240
OH-1004 ID	LXL04_039773
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	99.600
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_039773

Location JAJTUU010000039.1:248257-250505 (-)

Description Similar to BBX22: B-box zinc finger protein 22

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g78600`	Acts as a positive regulator of seedling photomorphogenesis and light-regulated inhibition of hypocotyl elongation, independently and in concert with HY5 and BBX21.	LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation.2008 · DOI: 10.1111/j.1365-313x.2008.03401.x The common function of a novel subfamily of B-Box zinc finger proteins with reference to circadian-associated events in Arabidopsis thaliana.2008 · DOI: 10.1271/bbb.80041 LZF1/SALT TOLERANCE HOMOLOG3, an Arabidopsis B-box protein involved in light-dependent development and gene expression, undergoes COP1-mediated ubiquitination.2008 · DOI: 10.1105/tpc.108.061747 COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis.2011 · DOI: 10.1104/pp.111.175042
`At2g31380`	Acts as a negative regulator of seedling photomorphogenesis.	The Arabidopsis B-BOX protein BBX25 interacts with HY5, negatively regulating BBX22 expression to suppress seedling photomorphogenesis.2013 · DOI: 10.1105/tpc.113.109751
`At1g06040`	Acts as a negative regulator of seedling photomorphogenesis and light-regulated inhibition of hypocotyl elongation.	Nuclear localization and interaction with COP1 are required for STO/BBX24 function during photomorphogenesis.2011 · DOI: 10.1104/pp.111.180208 Arabidopsis STO/BBX24 negatively regulates UV-B signaling by interacting with COP1 and repressing HY5 transcriptional activity.2012 · DOI: 10.1038/cr.2012.34 The Arabidopsis B-BOX protein BBX25 interacts with HY5, negatively regulating BBX22 expression to suppress seedling photomorphogenesis.2013 · DOI: 10.1105/tpc.113.109751
`At4g10240`	Probable transcription factor that may be involved in seedling photomorphogenesis.	No verified direct reference in this release
`At1g75540`	Transcription activator that acts as a positive regulator of seedling photomorphogenesis.	SALT TOLERANCE HOMOLOG2, a B-box protein in Arabidopsis that activates transcription and positively regulates light-mediated development.2007 · DOI: 10.1105/tpc.107.054791

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_039773 · 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:0009416 response to light stimulus Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009641 shade avoidance Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009718 anthocyanin-containing compound biosynthetic process Biological Process

GO:0010100 negative regulation of photomorphogenesis Biological Process

GO:0010117 photoprotection Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0015995 chlorophyll biosynthetic process Biological Process

GO:0048573 photoperiodism, flowering Biological Process

KEGG gene cross-reference

ath:AT1G06040

ath:AT1G75540

ath:AT1G78600

ath:AT2G31380

ath:AT4G10240

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.

Nucleus0.617

Rank 1 · LXL04_039773 · OH-1004

Cytoplasm0.412

Rank 2 · LXL04_039773 · OH-1004

Cell membrane0.076

Rank 3 · LXL04_039773 · OH-1004

Endoplasmic reticulum0.071

Rank 4 · LXL04_039773 · OH-1004

Golgi apparatus0.044

Rank 5 · LXL04_039773 · 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.

PF00643.30zf-B_box3-46 aa

PF00643.30zf-B_box53-94 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039773	`PF00643.30`	zf-B_box	3	46	2.8e-13	50.5
LXL04_039773	`PF00643.30`	zf-B_box	53	94	2.8e-13	50.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SYM2`	Arabidopsis thaliana	B-box zinc finger protein 22	50.338%	Swiss-Prot	strong database homology
`Q9SID1`	Arabidopsis thaliana	B-box zinc finger protein 25	42.466%	Swiss-Prot	moderate database homology
`Q96288`	Arabidopsis thaliana	B-box zinc finger protein 24	65.714%	Swiss-Prot	weak database homology
`O82617`	Arabidopsis thaliana	B-box zinc finger protein 23	60.526%	Swiss-Prot	weak database homology
`Q9LQZ7`	Arabidopsis thaliana	B-box zinc finger protein 21	54.464%	Swiss-Prot	weak database homology

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