Leaf Senescence DataBase

Basic information

Locus name

AT4G39850

Organism

Arabidopsis thaliana

Taxonomic identifier

[NCBI]

Function category

Lipid/Carbohydrate metabolism

Effect for Senescence

unclear

Gene Description

peroxisomal ABC transporter (PXA1) identical to peroxisomal ABC transporter PXA1 GI:15320529 from [Arabidopsis thaliana]; contains Pfam profile PF00005: ABC transporter;

Evidence

Genomic evidence:microarray data [Ref 1]

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

Gene Ontology

biological process	transport
cellular component	membrane
molecular function	ATP binding ATPase activity

Sequence

AT4G39850.1 | Genomic | mRNA | CDS | Protein

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: AT4G39850.1
miRNA: ath-miR447a
miRNA: ath-miR447a
mfe: -26.1 kcal/mol
p-value: 0.068237

position:  52
target 5' G   U  U          G   U 3'
           GAC AG ACGUCUCGUU CCG
           UUG UU UGUAGAGCAG GGU
miRNA  3' G      U          G   U 5'

target: AT4G39850.1
miRNA: ath-miR447b
miRNA: ath-miR447b
mfe: -26.1 kcal/mol
p-value: 0.065136

position:  52
target 5' G   U  U          G   U 3'
           GAC AG ACGUCUCGUU CCG
           UUG UU UGUAGAGCAG GGU
miRNA  3' G      U          G   U 5'

target: AT4G39850.1
miRNA: ath-miR854a
miRNA: ath-miR854a
mfe: -29.1 kcal/mol
p-value: 0.042618

position:  1
target 5'    U   U          C    U 3'
          CUC CUC CUCUCUAUCU UAUC
          GAG GAG GAGGGAUAGG GUAG
miRNA  3'                   A      5'

target: AT4G39850.1
miRNA: ath-miR854b
miRNA: ath-miR854b
mfe: -29.1 kcal/mol
p-value: 0.039502

position:  1
target 5'    U   U          C    U 3'
          CUC CUC CUCUCUAUCU UAUC
          GAG GAG GAGGGAUAGG GUAG
miRNA  3'                   A      5'

target: AT4G39850.1
miRNA: ath-miR854c
miRNA: ath-miR854c
mfe: -29.1 kcal/mol
p-value: 0.040829

position:  1
target 5'    U   U          C    U 3'
          CUC CUC CUCUCUAUCU UAUC
          GAG GAG GAGGGAUAGG GUAG
miRNA  3'                   A      5'

target: AT4G39850.1
miRNA: ath-miR854d
miRNA: ath-miR854d
mfe: -29.1 kcal/mol
p-value: 0.046853

position:  1
target 5'    U   U          C    U 3'
          CUC CUC CUCUCUAUCU UAUC
          GAG GAG GAGGGAUAGG GUAG
miRNA  3'                   A      5'

target: AT4G39850.1
miRNA: ath-miR854e
miRNA: ath-miR854e
mfe: -29.1 kcal/mol
p-value: 0.041908

position:  1
target 5'    U   U          C    U 3'
          CUC CUC CUCUCUAUCU UAUC
          GAG GAG GAGGGAUAGG GUAG
miRNA  3'                   A      5'

Ortholog Group

Ortholog Groups: OG5_126726

Accession	Taxon
NP_175837	Arabidopsis thaliana
NP_568072 ( AT4G39850 )	Arabidopsis thaliana
CMC011C	Cyanidioschyzon merolae strain 10D
CME117C	Cyanidioschyzon merolae strain 10D
CMP028C	Cyanidioschyzon merolae strain 10D
99858	Chlamydomonas reinhardtii
ACO65758	Micromonas sp. RCC299
ACO70668	Micromonas sp. RCC299
NP_001042413	Oryza sativa Japonica Group
NP_001054425	Oryza sativa Japonica Group
1300010309	Ostreococcus tauri
gw1.02.00.103.1	Ostreococcus tauri
e_gw1.218.8.1	Physcomitrella patens subsp. patens
e_gw1.54.328.1	Physcomitrella patens subsp. patens
e_gw1.84.172.1	Physcomitrella patens subsp. patens
estExt_Genewise1.C_1500091	Physcomitrella patens subsp. patens
estExt_Genewise1.C_360227	Physcomitrella patens subsp. patens
estExt_fgenesh2_pm.C_1050002	Physcomitrella patens subsp. patens
30162.m001256	Ricinus communis
30186.m001316	Ricinus communis
estExt_thaps1_ua_kg.C_chr_50101	Thalassiosira pseudonana CCMP1335
gw1.7.58.1	Thalassiosira pseudonana CCMP1335
thaps1_ua_kg.chr_8000025	Thalassiosira pseudonana CCMP1335
XP_002946419	Volvox carteri f. nagariensis
XP_002955325	Volvox carteri f. nagariensis
XP_002958444	Volvox carteri f. nagariensis

Cross Link

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PANTHER	PTHR11384	0.0	1	717	No hit	NA
Pfam	PF06472	4.4E-88	83	361	IPR010509	ABC transporter, N-terminal
SUPERFAMILY	SSF90123	2.1E-8	145	419	IPR011527	ABC transporter, transmembrane domain, type 1
ProSiteProfiles	PS50929	9.9	153	343	IPR017940	ABC transporter, integral membrane type 1
SUPERFAMILY	SSF52540	3.2E-36	444	652	IPR027417	P-loop containing nucleoside triphosphate hydrolase
ProSiteProfiles	PS50893	14.1	448	695	IPR003439	ABC transporter-like
SMART	SM00382	3.8E-7	473	652	IPR003593	AAA+ ATPase domain
Pfam	PF00005	9.8E-9	488	610	IPR003439	ABC transporter-like
ProSitePatterns	PS00211	NA	582	596	IPR017871	ABC transporter, conserved site
Pfam	PF06472	7.5E-85	737	1012	IPR010509	ABC transporter, N-terminal
ProSiteProfiles	PS50929	9.6	760	998	IPR017940	ABC transporter, integral membrane type 1
SUPERFAMILY	SSF90123	1.2E-7	763	999	IPR011527	ABC transporter, transmembrane domain, type 1
ProSiteProfiles	PS50893	8.9	1091	1337	IPR003439	ABC transporter-like
SUPERFAMILY	SSF52540	1.4E-23	1095	1323	IPR027417	P-loop containing nucleoside triphosphate hydrolase
SMART	SM00382	0.2	1122	1333	IPR003593	AAA+ ATPase domain
Pfam	PF00005	2.0E-5	1170	1280	IPR003439	ABC transporter-like
ProSitePatterns	PS00211	NA	1252	1266	IPR017871	ABC transporter, conserved site

Subcellular Localization

Localization 1
	Localization	other cytoplasmic components
	Evidence	Localization with GFP-fusion protein (GFP:cDNA)
	Pubmed ID	10737809

Localization 2
	Localization	peroxisome
	Evidence	SUBAcon
	Pubmed ID	23180787