LXL04_001148 | RubberDandelionOmics

Gene overview

LXL04_001148

Reference: OH-1004 Chr: Chr01 Coordinates: 21105504-21106019 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

516 bp · LXL04_001148|LXL04_001148|OH1004|cDNA

ATGTTCTTCAAGCTACCGGCAAAAGCCCGATTACAAGAAGCGCTTACCCAAATGTGGCAGCATGAAGCTGCTTCTCGAGCGATTCTCGAAAACGGAGTAGAAGAAGGGCTTGGAGACTCGTCGGAAAGTGCACCGATAGCCTTCCAGCAAGACATGGACATGGAAATGGACGAGAATATCCTCAGGGCCAACCCTACGACCACCACAATCCGTCATTACGAAGACCAAATGGTTCCGAGTATGACGACCTCGTTGTTTAG...

CDS

Download CDS FASTA

516 bp · LXL04_001148|LXL04_001148|OH1004|CDS

ATGTTCTTCAAGCTACCGGCAAAAGCCCGATTACAAGAAGCGCTTACCCAAATGTGGCAGCATGAAGCTGCTTCTCGAGCGATTCTCGAAAACGGAGTAGAAGAAGGGCTTGGAGACTCGTCGGAAAGTGCACCGATAGCCTTCCAGCAAGACATGGACATGGAAATGGACGAGAATATCCTCAGGGCCAACCCTACGACCACCACAATCCGTCATTACGAAGACCAAATGGTTCCGAGTATGACGACCTCGTTGTTTAG...

Protein

Download Protein FASTA

171 aa · LXL04_001148|LXL04_001148|OH1004|PROTEIN

MFFKLPAKARLQEALTQMWQHEAASRAILENGVEEGLGDSSESAPIAFQQDMDMEMDENILRANPTTTTIRHYEDQMVPSMTTSLFRGGEEESSSEIGNLGEDSRAEVPINEGGDRQTVRTGNMQPPIDITRALSIADDLPADSSNSSSSSSRERDGGVVPMWSPSLAGFR

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_001148`
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_001148

Location Chr01:21105504-21106019 (-)

Description Similar to CRY1: Cryptochrome-1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g08920`	May act as a blue-light receptor regulating hypocotyl elongation, flowering and other light responses.	Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition of Hypocotyl Elongation.1991 · DOI: 10.1105/tpc.3.7.685 Cryptochrome photoreceptors cry1 and cry2 antagonistically regulate primary root elongation in Arabidopsis thaliana.2006 · DOI: 10.1007/s00425-006-0280-6 CRY1 inhibits COP1-mediated degradation of BIT1, a MYB transcription factor, to activate blue light-dependent gene expression in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03508.x CRYPTOCHROME 1 is implicated in promoting R protein-mediated plant resistance to Pseudomonas syringae in Arabidopsis.2010 · DOI: 10.1093/mp/ssp107 Arabidopsis cryptochrome-1 restrains lateral roots growth by inhibiting auxin transport.2010 · DOI: 10.1016/j.jplph.2009.12.003 Light receptor action is critical for maintaining plant biomass at warm ambient temperatures.2011 · DOI: 10.1111/j.1365-313x.2010.04434.x Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades.2011 · DOI: 10.1111/j.1365-313x.2011.04598.x Light-activated cryptochrome reacts with molecular oxygen to form a flavin-superoxide radical pair consistent with magnetoreception.2011 · DOI: 10.1074/jbc.m111.228940 Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response to blue light.2011 · DOI: 10.1101/gad.2025011 The Cryptochrome Blue Light Receptors.2010 · DOI: 10.1199/tab.0135 Light-induced conformational changes in full-length Arabidopsis thaliana cryptochrome.2011 · DOI: 10.1016/j.jmb.2011.08.031 Phototropins but not cryptochromes mediate the blue light-specific promotion of stomatal conductance, while both enhance photosynthesis and transpiration under full sunlight.2012 · DOI: 10.1104/pp.111.187237 The shoot regeneration capacity of excised Arabidopsis cotyledons is established during the initial hours after injury and is modulated by a complex genetic network of light signalling.2013 · DOI: 10.1111/j.1365-3040.2012.02554.x The CRYPTOCHROME1-dependent response to excess light is mediated through the transcriptional activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis.2012 · DOI: 10.1105/tpc.112.100099 cry1 and GPA1 signaling genetically interact in hook opening and anthocyanin synthesis in Arabidopsis.2012 · DOI: 10.1007/s11103-012-9950-x Lifetimes of Arabidopsis cryptochrome signaling states in vivo.2013 · DOI: 10.1111/tpj.12144 Strigolactone-regulated hypocotyl elongation is dependent on cryptochrome and phytochrome signaling pathways in Arabidopsis.2014 · DOI: 10.1093/mp/sst093 Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome may define a novel evolutionarily conserved signaling mechanism.2015 · DOI: 10.1111/nph.13341 Suppression of Arabidopsis flowering by near-null magnetic field is affected by light.2015 · DOI: 10.1002/bem.21927 Cellular metabolites modulate in vivo signaling of Arabidopsis cryptochrome-1.2015 · DOI: 10.1080/15592324.2015.1063758 Mutations throughout an Arabidopsis blue-light photoreceptor impair blue-light-responsive anthocyanin accumulation and inhibition of hypocotyl elongation.1995 · DOI: 10.1046/j.1365-313x.1995.08050653.x Cryptochrome blue-light photoreceptors of Arabidopsis implicated in phototropism.1998 · DOI: 10.1038/33701 Genetic interactions between phytochrome A, phytochrome B, and cryptochrome 1 during Arabidopsis development.1998 · DOI: 10.1104/pp.118.1.27

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_001148 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006952 defense response Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009266 response to temperature stimulus Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009583 detection of light stimulus Biological Process

GO:0009637 response to blue light Biological Process

GO:0009638 phototropism Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009644 response to high light intensity Biological Process

GO:0009646 response to absence of light Biological Process

GO:0009785 blue light signaling pathway Biological Process

KEGG gene cross-reference

ath:AT4G08920

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.

Nucleus0.524

Rank 1 · LXL04_001148 · OH-1004

Cytoplasm0.437

Rank 2 · LXL04_001148 · OH-1004

Cell membrane0.090

Rank 3 · LXL04_001148 · OH-1004

Mitochondrion0.067

Rank 4 · LXL04_001148 · OH-1004

Endoplasmic reticulum0.053

Rank 5 · LXL04_001148 · 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.

PF12546.14Cryptochrome_C44-121 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001148	`PF12546.14`	Cryptochrome_C	44	121	6.9e-25	88.7

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
`Q43125`	Arabidopsis thaliana	Cryptochrome-1	62.037%	Swiss-Prot	moderate database homology

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