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BaseInfo

ncRNA ID ath-miR400
Species Arabidopsis thaliana
Class miRNA
Genome position chr1:11785936-11786037 [+]
Reference genome TAIR10
Source miRBase
Length 21
Mature sequence(if miRNA) 12 - UAUGAGAGUAUUAUAAGUCAC - 32
Stem-loop(if miRNA) --U    A UG         G              A A    GU      A
   GAGG U  UUUAUGAGA UAUUAUAAGUCACU C UUUG  AAGCAA G
   |||| |  ||||||||| |||||||||||||| | ||||  ||||||
   UUUU G  AAGUACUCU AUAGUAUUCAGUGA G AAAC  UUUGUU U
ACG    A GU         A              A C    UC      G
Stem-loop sequence UGAGGAUUGUUUAUGAGAGUAUUAUAAGUCACUACAUUUGGUAAGCAAAGUGUUGUUUCUCAAACGAAGUGACUUAUGAUAAUCUCAUGAAUGGAUUUUGCA

Targets Info

Target Acc Alignment Exception Target Description Target Gene Name Target Type Method
NM_100537.4
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |||||||||||||||||||||
targets:1304   GUGACUUAUAAUACUCUCAUA   1324

0.0 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G06580) coding protein psRNATarget
NM_001331633.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |||||||||||||||||||||
targets:1111   GUGACUUAUAAUACUCUCAUA   1131

0.0 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G06580) coding protein psRNATarget
NM_001331634.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |||||||||||||||||||||
targets:1108   GUGACUUAUAAUACUCUCAUA   1128

0.0 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G06580) coding protein psRNATarget
AK229240.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |||||||||||||||||||||
targets:1086   GUGACUUAUAAUACUCUCAUA   1106

0.0 Arabidopsis thaliana mRNA for hypothetical protein, clone: RAFL16-52-L06 NA coding protein psRNATarget
AK221583.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||||||||||||||||||||*
targets:985   GUGACUUAUAAUACUCUCAUU   1005

1.0 Arabidopsis thaliana mRNA for PPR-repeat protein, complete cds, clone: RAFL07-84-B14 NA coding protein psRNATarget
NM_104949.2
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||||||||||||||||||||*
targets:985   GUGACUUAUAAUACUCUCAUU   1005

1.0 Arabidopsis thaliana Pentatricopeptide repeat (PPR-like) superfamily protein (NG1), mRNA Pentatricopeptide repeat (PPR-like) superfamily protein(NG1) coding protein psRNATarget
BT012561.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||||||||||||||||||||*
targets:766   GUGACUUAUAAUACUCUCAUU   786

1.0 Arabidopsis thaliana At1g62720 gene, complete cds NA coding protein psRNATarget
AK221654.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||*||*|||||||||||||||
targets:1250   GUUACAUAUAAUACUCUCAUA   1270

2.0 Arabidopsis thaliana mRNA for putative membrane-associated salt-inducible protein, complete cds, clone: RAFL09-42-P03 NA coding protein psRNATarget
NM_104937.3
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||*||*|||||||||||||||
targets:1251   GUUACAUAUAAUACUCUCAUA   1271

2.0 Arabidopsis thaliana pentatricopeptide (PPR) repeat-containing protein mRNA pentatricopeptide (PPR) repeat-containing protein(AT1G62590) coding protein psRNATarget
AY136399.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||*||*|||||||||||||||
targets:1250   GUUACAUAUAAUACUCUCAUA   1270

2.0 Arabidopsis thaliana putative membrane-associated salt-inducible protein (At1g62590) mRNA, complete cds NA coding protein psRNATarget
NM_001334041.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||*||*|||||||||||||||
targets:1251   GUUACAUAUAAUACUCUCAUA   1271

2.0 Arabidopsis thaliana pentatricopeptide (PPR) repeat-containing protein partial mRNA pentatricopeptide (PPR) repeat-containing protein(AT1G62590) coding protein psRNATarget
NM_001334079.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |**||*|||||||||||||||
targets:976   GAUACAUAUAAUACUCUCAUA   996

2.0 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein partial mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G63330) coding protein psRNATarget
NM_001334080.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |**||*|||||||||||||||
targets:976   GAUACAUAUAAUACUCUCAUA   996

2.0 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein partial mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G63330) coding protein psRNATarget
NM_105012.3
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |**||*|||||||||||||||
targets:1011   GAUACAUAUAAUACUCUCAUA   1031

2.0 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein partial mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G63330) coding protein psRNATarget
NM_112544.3
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||||=|||||*||||||||||
targets:1113   GUGAUUUAUACUACUCUCAUA   1133

2.5 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein partial mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT3G16710) coding protein psRNATarget
NM_001338253.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  ||||=|||||*||||||||||
targets:1144   GUGAUUUAUACUACUCUCAUA   1164

2.5 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT3G16710) coding protein psRNATarget
NM_001332567.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |||||*|||||||||||*|||
targets:1442   GUGACCUAUAAUACUCUAAUA   1462

2.5 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G22960) coding protein psRNATarget
NM_001332568.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |||||*|||||||||||*|||
targets:1442   GUGACCUAUAAUACUCUAAUA   1462

2.5 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G22960) coding protein psRNATarget
AK230416.1
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |||||*|||||*|||||||||
targets:1053   GUGACCUAUAACACUCUCAUA   1073

2.5 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL25-31-I10 NA coding protein psRNATarget
NM_105133.2
ncRNA:21   CACUGAAUAUUAUGAGAGUAU   1
  |||||*|||||*|||||||||
targets:1055   GUGACCUAUAACACUCUCAUA   1075

2.5 Arabidopsis thaliana Pentatricopeptide repeat (PPR) superfamily protein mRNA Pentatricopeptide repeat (PPR) superfamily protein(AT1G64580) coding protein psRNATarget
NM_001341339.1
ncRNA:21   CA-CUGAAUAUUAUGAGAGUAU   1
  ||-|||*|||||||||||||||
targets:1341   GUCGACGUAUAAUACUCUCAUA   1362

3.0 Arabidopsis thaliana Tetratricopeptide repeat (TPR)-like superfamily protein mRNA Tetratricopeptide repeat (TPR)-like superfamily protein(AT4G19440) coding protein psRNATarget
NM_001341340.1
ncRNA:21   CA-CUGAAUAUUAUGAGAGUAU   1
  ||-|||*|||||||||||||||
targets:1341   GUCGACGUAUAAUACUCUCAUA   1362

3.0 Arabidopsis thaliana Tetratricopeptide repeat (TPR)-like superfamily protein mRNA Tetratricopeptide repeat (TPR)-like superfamily protein(AT4G19440) coding protein psRNATarget
NM_118064.2
ncRNA:21   CA-CUGAAUAUUAUGAGAGUAU   1
  ||-|||*|||||||||||||||
targets:1341   GUCGACGUAUAAUACUCUCAUA   1362

3.0 Arabidopsis thaliana Tetratricopeptide repeat (TPR)-like superfamily protein mRNA Tetratricopeptide repeat (TPR)-like superfamily protein(AT4G19440) coding protein psRNATarget
NM_001203842.2
ncRNA:21   CA-CUGAAUAUUAUGAGAGUAU   1
  ||-|||*|||||||||||||||
targets:1341   GUCGACGUAUAAUACUCUCAUA   1362

3.0 Arabidopsis thaliana Tetratricopeptide repeat (TPR)-like superfamily protein mRNA Tetratricopeptide repeat (TPR)-like superfamily protein(AT4G19440) coding protein psRNATarget
AY056145.1
ncRNA:21   CA-CUGAAUAUUAUGAGAGUAU   1
  ||-|||*|||||||||||||||
targets:1237   GUCGACGUAUAAUACUCUCAUA   1258

3.0 Arabidopsis thaliana unknown protein (At4g19440) mRNA, complete cds NA coding protein psRNATarget

Reference

1 PMID:15258262
"Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis";
Sunkar R, Zhu JK;
Plant Cell. 16:2001-2019(2004).
2 PMID:16954541
"MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant";
Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC;
Genome Res. 16:1276-1288(2006).
3 PMID:17182867
"A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana";
Rajagopalan R, Vaucheret H, Trejo J, Bartel DP;
Genes Dev. 20:3407-3425(2006).
4 PMID:19815687
"Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis";
Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, Wilson IW;
J Exp Bot. 61:165-177(2010).
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