Basic information   
Locus name AT4G13250
AliasNYC1
OrganismArabidopsis thaliana
Taxonomic identifier[NCBI]
Function categoryChlorophyll degradation
Effect for Senescencepromote
Gene DescriptionEncodes a chlorophyll b reductase involved in the degradation of chlorophyll b and LHCII (light harvesting complex II).
EvidenceMolecular evidence: SSH and Northern [Ref 1]
References
1: Gepstein S, Sabehi G, Carp MJ, Hajouj T, Nesher MF, Yariv I, Dor C, Bassani M
Large-scale identification of leaf senescence-associated genes.
Plant J. 2003 Dec;36(5):629-42

Gene Ontology
biological process
molecular function
Protein-Protein Interaction
STRING
SequenceAT4G13250.1 | Genomic | mRNA | CDS | Protein
Mutant information   
Mutant name 35S-NYC1-GFP
Mutant/Transgenic transgenic
Ecotype Col-0
Mutagenesis type transgene
Microarray   
Expression Level (Log2 ratio)
Sampling Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, Nam HG, Lin JF, Wu SH, Swidzinski J, Ishizaki K, Leaver CJ.
Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis.
Plant J. 2005 May;42(4)
Comparation Legends:
Col: wild type, indicates the ratio of expression in senescing leaves/green leaves.
NahG, coi1 and ein2: indicates the ratio of expression in senescing leaves of mutant/senescing wild type.
D/L: ratio of DARK 5d/control.
CD: Cell Death, ratio of starved cell suspension culture/control.
Genes showing at least 3 fold (ratio) up regulation during leaf senescence.
miRNA Interaction      
Details
target: AT4G13250.1 
miRNA: ath-miR156a
mfe: -25.2 kcal/mol 
p-value: 0.031609 

position:  1600 
target 5' C     U      U      G 3' 
           UGUUU CUCUCU UCUGUU  
           ACGAG GAGAGA AGACAG  
miRNA  3' C     U             U 5' 

target: AT4G13250.1 
miRNA: ath-miR156b
mfe: -25.2 kcal/mol 
p-value: 0.034328 

position:  1600 
target 5' C     U      U      G 3' 
           UGUUU CUCUCU UCUGUU  
           ACGAG GAGAGA AGACAG  
miRNA  3' C     U             U 5' 

target: AT4G13250.1 
miRNA: ath-miR156c
mfe: -25.2 kcal/mol 
p-value: 0.023708 

position:  1600 
target 5' C     U      U      G 3' 
           UGUUU CUCUCU UCUGUU  
           ACGAG GAGAGA AGACAG  
miRNA  3' C     U             U 5' 

target: AT4G13250.1 
miRNA: ath-miR156d
mfe: -25.2 kcal/mol 
p-value: 0.032345 

position:  1600 
target 5' C     U      U      G 3' 
           UGUUU CUCUCU UCUGUU  
           ACGAG GAGAGA AGACAG  
miRNA  3' C     U             U 5' 

target: AT4G13250.1 
miRNA: ath-miR156e
mfe: -25.2 kcal/mol 
p-value: 0.027013 

position:  1600 
target 5' C     U      U      G 3' 
           UGUUU CUCUCU UCUGUU  
           ACGAG GAGAGA AGACAG  
miRNA  3' C     U             U 5' 

target: AT4G13250.1 
miRNA: ath-miR156f
mfe: -25.2 kcal/mol 
p-value: 0.031382 

position:  1600 
target 5' C     U      U      G 3' 
           UGUUU CUCUCU UCUGUU  
           ACGAG GAGAGA AGACAG  
miRNA  3' C     U             U 5' 

target: AT4G13250.1 
miRNA: ath-miR156g
mfe: -26.3 kcal/mol 
p-value: 0.018892 

position:  1600 
target 5' C     U       U      U 3' 
           UGUUU CUCUCUU CUGUUG  
           ACGAG GAGAGAA GACAGC  
miRNA  3' C     U                5' 
Ortholog Group      
Ortholog Groups: OG5_136329
AccessionTaxon
NP_567400 ( AT4G13250 ) Arabidopsis thaliana
NP_568145Arabidopsis thaliana
CMP155CCyanidioschyzon merolae strain 10D
194485Chlamydomonas reinhardtii
205572Chlamydomonas reinhardtii
ACO66601Micromonas sp. RCC299
ACO70117Micromonas sp. RCC299
NP_001042468Oryza sativa Japonica Group
NP_001050798Oryza sativa Japonica Group
1100010225Ostreococcus tauri
gw1.01.00.423.1Ostreococcus tauri
e_gw1.373.14.1Physcomitrella patens subsp. patens
estExt_Genewise1.C_1990001Physcomitrella patens subsp. patens
gw1.100.151.1Physcomitrella patens subsp. patens
29852.m002016Ricinus communis
29912.m005516Ricinus communis
fgenesh1_pg.C_chr_9000231Thalassiosira pseudonana CCMP1335
XP_002948073Volvox carteri f. nagariensis
XP_002956541Volvox carteri f. nagariensis
Cross Link      
DatabaseEntry IDE-valueStartEndInterPro IDDescription
PANTHERPTHR243147.0E-24346490No hitNA
PANTHERPTHR24314:SF37.0E-24346490No hitNA
Gene3DG3DSA:3.40.50.7204.2E-45161376IPR016040NAD(P)-binding domain
SUPERFAMILYSSF517357.5E-41161394No hitNA
PfamPF001061.8E-20163340IPR002198Short-chain dehydrogenase/reductase SDR
PRINTSPR000816.6E-14163180IPR002347Glucose/ribitol dehydrogenase
CoilsCoilNA195223No hitNA
PRINTSPR000816.6E-14254265IPR002347Glucose/ribitol dehydrogenase
PRINTSPR000816.6E-14303319IPR002347Glucose/ribitol dehydrogenase
PRINTSPR000816.6E-14330349IPR002347Glucose/ribitol dehydrogenase
PRINTSPR000816.6E-14351368IPR002347Glucose/ribitol dehydrogenase
Subcellular Localization   
Localizationcytosol
EvidenceSUBAcon
Pubmed ID23180787

© Center for Bioinformatics(CBI), Peking University