Leaf Senescence DataBase

Basic information

Locus name

AT3G55770

Organism

Arabidopsis thaliana

Taxonomic identifier

[NCBI]

Function category

Others

Effect for Senescence

unclear

Gene Description

LIM domain-containing protein; FUNCTIONS IN: zinc ion binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, LIM-type (InterPro:IPR001781); BEST Arabidopsis thaliana protein match is: LIM domain-containing protein (TAIR:AT2G39900.1); Has 4177 Blast hits to 2942 proteins in 147 species: Archae - 0; Bacteria - 0; Metazoa - 3497; Fungi - 56; Plants - 295; Viruses - 0; Other Eukaryotes - 329 (source: NCBI BLink).

Evidence

Genomic evidence:microarray data [Ref 1]

References

1: Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, Hill C, Kiddle S, Kim YS, Penfold CA, Jenkins D, Zhang C, Morris K, Jenner C, Jackson S, Thomas B, Tabrett A, Legaie R, Moore JD, Wild DL, Ott S, Rand D, Beynon J, Denby K, Mead A, Buchanan-Wollaston
High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation.
Plant Cell 2011 Mar;23(3):873-94

Gene Ontology

molecular function

zinc ion binding

Sequence

miRNA Interaction

Details

target: AT3G55770.1
miRNA: ath-miR5658
miRNA: ath-miR5658
mfe: -30.0 kcal/mol
p-value: 0.000328

position: 119
target 5' C      C            C  3'
           UUCGUC UCAUCAUCGUCA
           AAGUAG AGUAGUAGUAGU
miRNA  3' A      U            A  5'

target: AT3G55770.4
miRNA: ath-miR5658
miRNA: ath-miR5658
mfe: -30.0 kcal/mol
p-value: 0.000308

position: 36
target 5' C      C            C  3'
           UUCGUC UCAUCAUCGUCA
           AAGUAG AGUAGUAGUAGU
miRNA  3' A      U            A  5'

target: AT3G55770.6
miRNA: ath-miR5658
miRNA: ath-miR5658
mfe: -30.0 kcal/mol
p-value: 0.000444

position: 102
target 5' C      C            C  3'
           UUCGUC UCAUCAUCGUCA
           AAGUAG AGUAGUAGUAGU
miRNA  3' A      U            A  5'

target: AT3G55770.7
miRNA: ath-miR5658
miRNA: ath-miR5658
mfe: -30.0 kcal/mol
p-value: 0.000330

position: 136
target 5' C      C            C  3'
           UUCGUC UCAUCAUCGUCA
           AAGUAG AGUAGUAGUAGU
miRNA  3' A      U            A  5'

Ortholog Group

Ortholog Groups: OG5_128738

Accession	Taxon
NP_001030868	Arabidopsis thaliana
NP_001030869	Arabidopsis thaliana
NP_001030870 ( AT3G55770 )	Arabidopsis thaliana
NP_171683	Arabidopsis thaliana
NP_181519	Arabidopsis thaliana
NP_191136	Arabidopsis thaliana
NP_680133	Arabidopsis thaliana
ACO65302	Micromonas sp. RCC299
NP_001047550	Oryza sativa Japonica Group
NP_001049655	Oryza sativa Japonica Group
NP_001053405	Oryza sativa Japonica Group
NP_001064995	Oryza sativa Japonica Group
fgenesh1_pg.C_Chr_12.0001000188	Ostreococcus tauri
e_gw1.65.246.1	Physcomitrella patens subsp. patens
estExt_fgenesh2_pg.C_1360050	Physcomitrella patens subsp. patens
fgenesh1_pg.scaffold_80000002	Physcomitrella patens subsp. patens
29610.m000403	Ricinus communis
29812.m000202	Ricinus communis
30174.m008997	Ricinus communis

Cross Link

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SUPERFAMILY	SSF57716	6.3E-9	3	35	No hit	NA
ProSiteProfiles	PS50023	13.8	8	68	IPR001781	Zinc finger, LIM-type
SMART	SM00132	5.4E-13	9	61	IPR001781	Zinc finger, LIM-type
PANTHER	PTHR24206	3.7E-19	10	67	No hit	NA
Pfam	PF00412	7.9E-14	10	65	IPR001781	Zinc finger, LIM-type
ProSitePatterns	PS00478	NA	10	44	IPR001781	Zinc finger, LIM-type
SUPERFAMILY	SSF57716	1.5E-14	36	76	No hit	NA
SUPERFAMILY	SSF57716	2.2E-9	101	133	No hit	NA
ProSiteProfiles	PS50023	12.6	106	166	IPR001781	Zinc finger, LIM-type
SMART	SM00132	1.2E-13	107	159	IPR001781	Zinc finger, LIM-type
Pfam	PF00412	5.0E-14	108	164	IPR001781	Zinc finger, LIM-type
SUPERFAMILY	SSF57716	2.2E-14	134	173	No hit	NA

Subcellular Localization

Localization

cytosol

Evidence

SUBAcon

Pubmed ID

23180787