Leaf Senescence DataBase

Basic information

Locus name

AT5G10650

Organism

Arabidopsis thaliana

Taxonomic identifier

[NCBI]

Function category

Others

Effect for Senescence

unclear

Gene Description

zinc finger (C3HC4-type RING finger) family protein similar to Pfam domain, PF00097: Zinc finger, C3HC4 type (RING finger)

Evidence

Genomic evidence:microarray data [Ref 1]; Molecular evidence: SSH and Northern [Ref 2]

References

1: 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):567-85

2: 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

molecular function

Sequence

Microarray

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: AT5G10650.1
miRNA: ath-miR162a
miRNA: ath-miR162a
mfe: -27.2 kcal/mol
p-value: 0.007704

position:  1200
target 5' A   A U         A       C 3'
           UGG A UGCAGAGGU UUGUUGG
           ACC U ACGUCUCCA AAUAGCU
miRNA  3' G                         5'

target: AT5G10650.1
miRNA: ath-miR162b
miRNA: ath-miR162b
mfe: -27.2 kcal/mol
p-value: 0.003860

position:  1200
target 5' A   A U         A       C 3'
           UGG A UGCAGAGGU UUGUUGG
           ACC U ACGUCUCCA AAUAGCU
miRNA  3' G                         5'

target: AT5G10650.1
miRNA: ath-miR414
miRNA: ath-miR414
mfe: -24.7 kcal/mol
p-value: 0.011836

position:  1528
target 5' A    U   U            A 3'
           GA G AUG UGAUGGAGAUGA
           CU C UAC ACUACUUCUACU
miRNA  3' A  G     U              5'

target: AT5G10650.2
miRNA: ath-miR162a
miRNA: ath-miR162a
mfe: -27.2 kcal/mol
p-value: 0.007808

position:  1225
target 5' A   A U         A       C 3'
           UGG A UGCAGAGGU UUGUUGG
           ACC U ACGUCUCCA AAUAGCU
miRNA  3' G                         5'

target: AT5G10650.2
miRNA: ath-miR162b
miRNA: ath-miR162b
mfe: -27.2 kcal/mol
p-value: 0.003931

position:  1225
target 5' A   A U         A       C 3'
           UGG A UGCAGAGGU UUGUUGG
           ACC U ACGUCUCCA AAUAGCU
miRNA  3' G                         5'

target: AT5G10650.2
miRNA: ath-miR414
miRNA: ath-miR414
mfe: -24.7 kcal/mol
p-value: 0.012016

position:  1553
target 5' A    U   U            A 3'
           GA G AUG UGAUGGAGAUGA
           CU C UAC ACUACUUCUACU
miRNA  3' A  G     U              5'

Ortholog Group

Ortholog Groups: OG5_160013

Accession	Taxon
NP_001031869 ( AT5G10650 )	Arabidopsis thaliana
NP_196626	Arabidopsis thaliana
NP_568462	Arabidopsis thaliana
NP_974832	Arabidopsis thaliana
NP_001045903	Oryza sativa Japonica Group
NP_001058451	Oryza sativa Japonica Group
29848.m004449	Ricinus communis

Cross Link

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PANTHER	PTHR14155	9.5E-157	266	524	No hit	NA
SUPERFAMILY	SSF57850	1.8E-19	466	519	No hit	NA
Pfam	PF13639	2.6E-14	474	517	IPR001841	Zinc finger, RING-type
ProSiteProfiles	PS50089	12.2	475	516	IPR001841	Zinc finger, RING-type
SMART	SM00184	1.6E-6	475	515	IPR001841	Zinc finger, RING-type