LXL04_005154 | RubberDandelionOmics

Gene overview

LXL04_005154

Reference: OH-1004 Chr: Chr01 Coordinates: 156633501-156636724 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1305 bp · LXL04_005154|LXL04_005154|OH1004|cDNA

ATGGAGTTATCTCCCATTCGGTTTCTAAATCGCACAGACGCACAGTTCCCTTCTCTTCTCCTCTTCTCCTCTTCAGTCGACCGTCTTCAATTTCCAAATCAAACCTCAAGCTGTCAAGCATCGTCGAGCATCTCAGTGTCTCACTCAAGCGTCGCTCACTCTGTCCATCATTCTCGGTTCGAGATTGATACAGGACAGCTAACATCAGCCGCTGACTTGGACTTGTGTTTAGGGGCAACTAACATCACTAGTTTACTACA...

CDS

Download CDS FASTA

1305 bp · LXL04_005154|LXL04_005154|OH1004|CDS

ATGGAGTTATCTCCCATTCGGTTTCTAAATCGCACAGACGCACAGTTCCCTTCTCTTCTCCTCTTCTCCTCTTCAGTCGACCGTCTTCAATTTCCAAATCAAACCTCAAGCTGTCAAGCATCGTCGAGCATCTCAGTGTCTCACTCAAGCGTCGCTCACTCTGTCCATCATTCTCGGTTCGAGATTGATACAGGACAGCTAACATCAGCCGCTGACTTGGACTTGTGTTTAGGGGCAACTAACATCACTAGTTTACTACA...

Protein

Download Protein FASTA

434 aa · LXL04_005154|LXL04_005154|OH1004|PROTEIN

MELSPIRFLNRTDAQFPSLLLFSSSVDRLQFPNQTSSCQASSSISVSHSSVAHSVHHSRFEIDTGQLTSAADLDLCLGATNITSLLHQLIKTKSRGQKLQIVVVVLRSEKMSGAGKTVCVTGASGYIASNLVKLLLHRGYAVKASVRYPNNPVKTEHLLKLDGAKERLHLFKADLLEEGSFDAAIDGCDGVFHTASPFLTSAADPQKELIEPALKGTLNVLGSCSKASSVKRVVVTSSLAAVAFNANPRTPDVVIDETWF...

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_005154`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_005154

Location Chr01:156633501-156636724 (-)

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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005154 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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: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

mtr:11424763

mtr:11427940

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.

Cytoplasm0.612

Rank 1 · LXL04_005154 · OH-1004

Nucleus0.285

Rank 2 · LXL04_005154 · OH-1004

Endoplasmic reticulum0.099

Rank 3 · LXL04_005154 · OH-1004

Plastid0.087

Rank 4 · LXL04_005154 · OH-1004

Cell membrane0.076

Rank 5 · LXL04_005154 · 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.

PF05368.20NmrA116-214 aa

PF01370.28Epimerase118-355 aa

PF01073.263Beta_HSD120-350 aa

PF07993.19NAD_binding_4120-341 aa

PF16363.12GDP_Man_Dehyd120-356 aa

PF13460.13NAD_binding_10122-243 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005154	`PF05368.20`	NmrA	116	214	5.4e-10	40.1
LXL04_005154	`PF01370.28`	Epimerase	118	355	7.1e-25	88.5
LXL04_005154	`PF01073.26`	3Beta_HSD	120	350	2.1e-19	70.4
LXL04_005154	`PF07993.19`	NAD_binding_4	120	341	1.3e-11	44.9
LXL04_005154	`PF16363.12`	GDP_Man_Dehyd	120	356	1.7e-11	44.9
LXL04_005154	`PF13460.13`	NAD_binding_10	122	243	1.1e-11	45.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9S9N9`	Arabidopsis thaliana	Cinnamoyl-CoA reductase 1	51.393%	Swiss-Prot	strong database homology

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