LXL04_019934 | RubberDandelionOmics

Gene overview

LXL04_019934

Reference: OH-1004 Chr: Chr04 Coordinates: 44677575-44679126 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

603 bp · LXL04_019934|LXL04_019934|OH1004|cDNA

atggagAGATACAGTAACAAAGTTTCCTCTACTGAAAAGCTTAGCATCACAAAGAAAGATTTAGGGAATGATAACTATGGTCATCATGAGCTTATGGGTGACATCGGTGGAGGCGGTGGTGAAGAACGCAGTCACGGTGGAGGTTGTTTGAATGGGGATTTAAAGAAGAAGAAAGCTGGTCAGATTAGTGGTGGTTTGAACGGTGTCATAAGGTGTTGTCAAGCCGAAAAATGTGCTAGTGATTTAGCTGAGGCCAAACA...

CDS

Download CDS FASTA

603 bp · LXL04_019934|LXL04_019934|OH1004|CDS

ATGGAGAGATACAGTAACAAAGTTTCCTCTACTGAAAAGCTTAGCATCACAAAGAAAGATTTAGGGAATGATAACTATGGTCATCATGAGCTTATGGGTGACATCGGTGGAGGCGGTGGTGAAGAACGCAGTCACGGTGGAGGTTGTTTGAATGGGGATTTAAAGAAGAAGAAAGCTGGTCAGATTAGTGGTGGTTTGAACGGTGTCATAAGGTGTTGTCAAGCCGAAAAATGTGCTAGTGATTTAGCTGAGGCCAAACA...

Protein

Download Protein FASTA

200 aa · LXL04_019934|LXL04_019934|OH1004|PROTEIN

MERYSNKVSSTEKLSITKKDLGNDNYGHHELMGDIGGGGGEERSHGGGCLNGDLKKKKAGQISGGLNGVIRCCQAEKCASDLAEAKQYHRRHRVCEFHAKAQAAIVAGSSQRFCQQCSRFHELSEFDEAKRSCRRRLAGHNERRRKNSMEFKGTGKELMNIQLSRYVYLPCKCCNFITLLNFFLKKVSLKDVVPDNVVCM

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_019934`
TK1151 ID	TkA05G107150
OH-1004 ID	LXL04_019934
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	93.200
Protein coverage (%)	TK1151 87.978 / OH-1004 81.000 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_019934

Location Chr04:44677575-44679126 (+)

Description Similar to SPL12: Squamosa promoter-binding-like protein 12

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g60030`	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'.	An Arabidopsis SBP-domain fragment with a disrupted C-terminal zinc-binding site retains its tertiary structure.2006 · DOI: 10.1016/j.febslet.2006.03.014
`At3g15270`	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter.	Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3.2006 · DOI: 10.1242/dev.02521
`At1g53160`	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter.	Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3.2006 · DOI: 10.1242/dev.02521
`At2g33810`	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter.	Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains.2005 · DOI: 10.1016/j.jmb.2005.07.013 Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3.2006 · DOI: 10.1242/dev.02521 Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition.1997 · DOI: 10.1046/j.1365-313x.1997.12020367.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_019934 · 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:0009908 flower development Biological Process

GO:0009911 positive regulation of flower development Biological Process

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

GO:0010229 inflorescence development Biological Process

GO:0010262 somatic embryogenesis Biological Process

GO:0010321 regulation of vegetative phase change Biological Process

GO:0030154 cell differentiation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

KEGG gene cross-reference

ath:AT1G53160

ath:AT2G33810

ath:AT3G15270

ath:AT3G60030

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.

Nucleus0.922

Rank 1 · LXL04_019934 · OH-1004

Cytoplasm0.130

Rank 2 · LXL04_019934 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_019934 · OH-1004

Endoplasmic reticulum0.018

Rank 4 · LXL04_019934 · OH-1004

Mitochondrion0.014

Rank 5 · LXL04_019934 · 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.

PF03110.20SBP73-146 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019934	`PF03110.20`	SBP	73	146	1.7e-31	109.1

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
`Q9S7P5`	Arabidopsis thaliana	Squamosa promoter-binding-like protein 12	53.600%	Swiss-Prot	moderate database homology
`Q9S758`	Arabidopsis thaliana	Squamosa promoter-binding-like protein 5	75.294%	Swiss-Prot	weak database homology
`Q9S7A9`	Arabidopsis thaliana	Squamosa promoter-binding-like protein 4	60.952%	Swiss-Prot	moderate database homology
`P93015`	Arabidopsis thaliana	Squamosa promoter-binding-like protein 3	62.887%	Swiss-Prot	weak database homology

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