LXL04_009213 | RubberDandelionOmics

Gene overview

LXL04_009213

Reference: OH-1004 Chr: Chr02 Coordinates: 120555995-120558457 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1008 bp · LXL04_009213|LXL04_009213|OH1004|cDNA

ATGTCTCCGGCAACTACCCAAGTAATCTGTGTCACCGGCGCCGGCGGATTCATCGCCTCGTGGATGGTTAAATTGCTCTTGGAGAAAGGCTATATTGTCAGGGGAACCGTTAGGAATCCAGATGATCCAAAGAATAATCATTTGAGAGAGCTTGAAGGAGCGAAGGAGAGATTAACTCTATTCAAAGCCGATCTTCTCGATTTTGAAAGCTTACGTGAAGCCATTAACGGCTGTGATGGTGTTTTCCACACTGCTTCTCC...

CDS

Download CDS FASTA

1008 bp · LXL04_009213|LXL04_009213|OH1004|CDS

ATGTCTCCGGCAACTACCCAAGTAATCTGTGTCACCGGCGCCGGCGGATTCATCGCCTCGTGGATGGTTAAATTGCTCTTGGAGAAAGGCTATATTGTCAGGGGAACCGTTAGGAATCCAGATGATCCAAAGAATAATCATTTGAGAGAGCTTGAAGGAGCGAAGGAGAGATTAACTCTATTCAAAGCCGATCTTCTCGATTTTGAAAGCTTACGTGAAGCCATTAACGGCTGTGATGGTGTTTTCCACACTGCTTCTCC...

Protein

Download Protein FASTA

335 aa · LXL04_009213|LXL04_009213|OH1004|PROTEIN

MSPATTQVICVTGAGGFIASWMVKLLLEKGYIVRGTVRNPDDPKNNHLRELEGAKERLTLFKADLLDFESLREAINGCDGVFHTASPVTDDPEQMVEPAVIGTKNIIVAAAEAKVRRVVFTSSIGAVYMDPNRSPDDVVDESCWSDLEFCKNTKNWYCYGKAVAEQAAWEEAKARGVDLVALNPVLVLGPLLQPTVNASIIHILKYLTGSAKTYANSVQAYVHVRDVALAHILLFETPSANGRYLCAESVLHRGEVVEIL...

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_009213`
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_009213

Location Chr02:120555995-120558457 (+)

Description Similar to CCR1: Cinnamoyl-CoA reductase 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g15950`	Involved in the latter stages of lignin biosynthesis.	Cloning and characterization of irregular xylem4 (irx4): a severely lignin-deficient mutant of Arabidopsis.2001 · DOI: 10.1046/j.1365-313x.2001.01021.x Reassessment of effects on lignification and vascular development in the irx4 Arabidopsis mutant.2005 · DOI: 10.1016/j.phytochem.2004.12.016 Redirection of the phenylpropanoid pathway to feruloyl malate in Arabidopsis mutants deficient for cinnamoyl-CoA reductase 1.2008 · DOI: 10.1007/s00425-007-0669-x The simultaneous repression of CCR and CAD, two enzymes of the lignin biosynthetic pathway, results in sterility and dwarfism in Arabidopsis thaliana.2011 · DOI: 10.1093/mp/ssq045
`At1g80820`	Cinnamoyl-CoA reductase probably involved in the formation of phenolic compounds associated with the hypersensitive response.	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_009213 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006952 defense response Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009409 response to cold Biological Process

GO:0009699 phenylpropanoid biosynthetic process Biological Process

GO:0009809 lignin biosynthetic process Biological Process

GO:0010597 green leaf volatile biosynthetic process Biological Process

GO:0042754 negative regulation of circadian rhythm Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0000166 nucleotide binding Molecular Function

GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Molecular Function

GO:0016621 cinnamoyl-CoA reductase activity Molecular Function

KEGG gene cross-reference

ath:AT1G15950

ath:AT1G80820

mtr:11424763

mtr:25487973

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.

Cytoplasm0.769

Rank 1 · LXL04_009213 · OH-1004

Nucleus0.248

Rank 2 · LXL04_009213 · OH-1004

Endoplasmic reticulum0.079

Rank 3 · LXL04_009213 · OH-1004

Cell membrane0.068

Rank 4 · LXL04_009213 · OH-1004

Mitochondrion0.058

Rank 5 · LXL04_009213 · 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.

PF05368.20NmrA6-125 aa

PF01370.28Epimerase9-241 aa

PF02719.22Polysacc_synt_29-127 aa

PF01073.263Beta_HSD11-233 aa

PF16363.12GDP_Man_Dehyd11-259 aa

PF07993.19NAD_binding_411-193 aa

PF13460.13NAD_binding_1013-132 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009213	`PF05368.20`	NmrA	6	125	2.6e-14	54.2
LXL04_009213	`PF01370.28`	Epimerase	9	241	2.9e-28	99.6
LXL04_009213	`PF02719.22`	Polysacc_synt_2	9	127	3.7e-07	30.4
LXL04_009213	`PF01073.26`	3Beta_HSD	11	233	5.3e-23	82.1
LXL04_009213	`PF16363.12`	GDP_Man_Dehyd	11	259	5.2e-15	56.4
LXL04_009213	`PF07993.19`	NAD_binding_4	11	193	3.1e-10	40.4
LXL04_009213	`PF13460.13`	NAD_binding_10	13	132	1.5e-18	68.1

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
`Q9S9N9`	Arabidopsis thaliana	Cinnamoyl-CoA reductase 1	80.126%	Swiss-Prot	strong database homology
`Q9SAH9`	Arabidopsis thaliana	Cinnamoyl-CoA reductase 2	74.695%	Swiss-Prot	strong database homology

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