LXL04_023974 | RubberDandelionOmics

Gene overview

LXL04_023974

Reference: OH-1004 Chr: Chr05 Coordinates: 76382940-76384923 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1098 bp · LXL04_023974|LXL04_023974|OH1004|cDNA

ATGGGTGTCATACGAACAGACGAGCTTCGGAGAGCTGAGATCCAAGAGTTCCGCCGCATGCTCTTGTCCTGCTCCGGCGTTGTCCTCAAGGTTAGAAACGAAGAGGAGTACAACCGCCGGCGGGTGCCAGAAGCTAACAGAAACGAATATACAGTAGATCAGAAGCTTGTATGCGTCACAAGCGGCGTCTCTTTACTTGGTGTCGCTCTTGTGAAAAAACTCTTACTCAGAGGCTATTCCGCTCGAATCGTCGTCAACAA...

CDS

Download CDS FASTA

1098 bp · LXL04_023974|LXL04_023974|OH1004|CDS

ATGGGTGTCATACGAACAGACGAGCTTCGGAGAGCTGAGATCCAAGAGTTCCGCCGCATGCTCTTGTCCTGCTCCGGCGTTGTCCTCAAGGTTAGAAACGAAGAGGAGTACAACCGCCGGCGGGTGCCAGAAGCTAACAGAAACGAATATACAGTAGATCAGAAGCTTGTATGCGTCACAAGCGGCGTCTCTTTACTTGGTGTCGCTCTTGTGAAAAAACTCTTACTCAGAGGCTATTCCGCTCGAATCGTCGTCAACAA...

Protein

Download Protein FASTA

365 aa · LXL04_023974|LXL04_023974|OH1004|PROTEIN

MGVIRTDELRRAEIQEFRRMLLSCSGVVLKVRNEEEYNRRRVPEANRNEYTVDQKLVCVTSGVSLLGVALVKKLLLRGYSARIVVNNEEDVERLREMEITEEIGGASNITSNSTIGVVVAKLNERQSLMDAFDGCCAVFHTAAFIDPTGVSGYSKCMAEIEAKTAENIAEACAATSSVRNYVLTSSLLTCIWRDISDSNLSPVVDHNTWSDESFCNRKKLWYALGKLKAERVSYEIAKEKGLKLATICSGLTTGPRYFCT...

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_023974`
TK1151 ID	TkA06G193330
OH-1004 ID	LXL04_023974
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.600
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_023974

Location Chr05:76382940-76384923 (-)

Description Similar to SNL6: Cinnamoyl-CoA reductase-like SNL6

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g35420`	Involved in the biosynthesis of hydroxylated tetraketide compounds that serve as sporopollenin precursors (the main constituents of exine).	An anther-specific dihydroflavonol 4-reductase-like gene (DRL1) is essential for male fertility in Arabidopsis.2009 · DOI: 10.1111/j.1469-8137.2008.02692.x Analysis of TETRAKETIDE α-PYRONE REDUCTASE function in Arabidopsis thaliana reveals a previously unknown, but conserved, biochemical pathway in sporopollenin monomer biosynthesis.2010 · DOI: 10.1105/tpc.110.080036
`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

Reference gene ID	Possible function	Papers / DOI
`Os01g0639200`	Involved in defense response.	Rice Snl6, a cinnamoyl-CoA reductase-like gene family member, is required for NH1-mediated immunity to Xanthomonas oryzae pv. oryzae.2010 · DOI: 10.1371/journal.pgen.1001123
`Os02g0808800`	Involved in the latter stages of lignin biosynthesis.	Cinnamoyl-CoA reductase, a key enzyme in lignin biosynthesis, is an effector of small GTPase Rac in defense signaling in rice.2006 · DOI: 10.1073/pnas.0509875103

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_023974 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006694 steroid biosynthetic process Biological Process

GO:0006952 defense response Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009409 response to cold Biological Process

GO:0009555 pollen development Biological Process

GO:0009699 phenylpropanoid biosynthetic process Biological Process

GO:0009809 lignin biosynthetic process Biological Process

GO:0010584 pollen exine formation Biological Process

GO:0010597 green leaf volatile biosynthetic process Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0048316 seed development Biological Process

GO:0080110 sporopollenin biosynthetic process Biological Process

KEGG gene cross-reference

ath:AT1G15950

ath:AT4G35420

dosa:Os01g0639200

dosa:Os02g0808800

osa:4326581

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.

Cytoplasm0.449

Rank 1 · LXL04_023974 · OH-1004

Nucleus0.424

Rank 2 · LXL04_023974 · OH-1004

Plastid0.089

Rank 3 · LXL04_023974 · OH-1004

Cell membrane0.076

Rank 4 · LXL04_023974 · OH-1004

Endoplasmic reticulum0.053

Rank 5 · LXL04_023974 · 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.

PF01370.28Epimerase58-268 aa

PF01073.263Beta_HSD59-187 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_023974	`PF01370.28`	Epimerase	58	268	6.4e-07	29.7
LXL04_023974	`PF01073.26`	3Beta_HSD	59	187	1.3e-06	28.4

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
`Q500U8`	Arabidopsis thaliana	Tetraketide alpha-pyrone reductase 1	30.483%	Swiss-Prot	moderate database homology
`Q9S9N9`	Arabidopsis thaliana	Cinnamoyl-CoA reductase 1	35.338%	Swiss-Prot	moderate database homology
`Q0JKZ0`	Oryza sativa subsp. japonica	Cinnamoyl-CoA reductase-like SNL6	41.207%	Swiss-Prot	moderate database homology
`Q6K9A2`	Oryza sativa subsp. japonica	Cinnamoyl-CoA reductase 1	30.877%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card