TkA05G022950 | RubberDandelionOmics

Gene overview

TkA05G022950

Reference: TK1151 Chr: Chr05 Coordinates: 6207167-6208759 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

708 bp · TkA05G022950|TK1151|cDNA

ATGCTCGATCCTGCTATACTAGGAACCCAAAACGTATTAAAAGCATGTGTGAAGGTTAAAGTCAAGAAGGTCGTGGTTATGTCATCAGTCACCGCTGTTATGAACAATCCTAAATGGCCTCTAGGCCTTGAAATGGATGAAAGCTGTTGGTCAGATCCAGATTTTTGCAAAGCTAACGAGAAATGGTACGCTTTATCCAAGACTATTGCTGAGCGTGAAGCTTGGGAGTATGCAAAAAGAGTTGGATTAAACGTTGTGAC...

CDS

Download CDS FASTA

708 bp · TkA05G022950|TK1151|CDS

ATGCTCGATCCTGCTATACTAGGAACCCAAAACGTATTAAAAGCATGTGTGAAGGTTAAAGTCAAGAAGGTCGTGGTTATGTCATCAGTCACCGCTGTTATGAACAATCCTAAATGGCCTCTAGGCCTTGAAATGGATGAAAGCTGTTGGTCAGATCCAGATTTTTGCAAAGCTAACGAGAAATGGTACGCTTTATCCAAGACTATTGCTGAGCGTGAAGCTTGGGAGTATGCAAAAAGAGTTGGATTAAACGTTGTGAC...

Protein

Download Protein FASTA

235 aa · TkA05G022950|TK1151|PROTEIN

MLDPAILGTQNVLKACVKVKVKKVVVMSSVTAVMNNPKWPLGLEMDESCWSDPDFCKANEKWYALSKTIAEREAWEYAKRVGLNVVTICPTATLGPMLQSTLSGSNLLILSYIKDGITKTEDVERAVVDVRDLADAIFMLYEKQESEGRYICSSYSIMTKEFVAKVQSMFPNYDYPKNFTEPNQTERMLFNSKKLLDVGWNYRPLEETIIDTMKYFEEVGVANRLDTEIELEIKF

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	`TkA05G022950`
TK1151 ID	TkA05G022950
OH-1004 ID	LXL04_009213
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	35.600
Protein coverage (%)	TK1151 93.617 / OH-1004 66.269 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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA05G022950

Location Chr05:6207167-6208759 (-)

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

Reference gene ID	Possible function	Papers / DOI
`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_009213 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

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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.

Cytoplasm0.799

Rank 1 · TkA05G022950 · TK1151

Nucleus0.306

Rank 2 · TkA05G022950 · TK1151

Endoplasmic reticulum0.059

Rank 3 · TkA05G022950 · TK1151

Cell membrane0.047

Rank 4 · TkA05G022950 · TK1151

Mitochondrion0.042

Rank 5 · TkA05G022950 · TK1151

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.

PF07993NAD_binding_43-105 aa

PF02719Polysacc_synt_25-33 aa

PF01370Epimerase6-146 aa

PF010733Beta_HSD6-74 aa

PF13460NAD_binding_108-37 aa

PF16363GDP_Man_Dehyd59-217 aa

PF10149TM23188-159 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G022950	`PF07993`	NAD_binding_4	3	105	4.3e-05	23.5
TkA05G022950	`PF02719`	Polysacc_synt_2	5	33	0.0057	16.6
TkA05G022950	`PF01370`	Epimerase	6	146	3.7e-12	46.9
TkA05G022950	`PF01073`	3Beta_HSD	6	74	4.6e-07	29.9
TkA05G022950	`PF13460`	NAD_binding_10	8	37	0.28	11.8
TkA05G022950	`PF16363`	GDP_Man_Dehyd	59	217	0.029	14.6
TkA05G022950	`PF10149`	TM231	88	159	0.066	13.1

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	sp\|Q9S9N9\|CCR1_ARATH Cinnamoyl-CoA reductase 1	36.000%	Swiss-Prot	Medium
`Q6K9A2`	Oryza sativa subsp. japonica	sp\|Q6K9A2\|CCR1_ORYSJ Cinnamoyl-CoA reductase 1	32.200%	Swiss-Prot	Medium

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