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BaseInfo

ncRNA ID	ath-miR172d-3p
Species	Arabidopsis thaliana
Class	miRNA
Genome position	chr3:20587904-20588027 [+]
Reference genome	TAIR10
Source	miRBase
Length	21
Mature sequence(if miRNA)	88 - AGAAUCUUGAUGAUGCUGCAG - 108
Stem-loop(if miRNA)	-GU    UA     A    U         AG        UUCUCU  U      UC AGUCAUU   UUGC  UUGCA CAUC UCAAGAUUC  AAAUCAGA      UA GGGUUU  U |||||||   ||||  ||||| |||| |||||||||  ||||||||      || |||||| UCGGUAA   AACG  GACGU GUAG AGUUCUAAG  UUUGGUUU      AU UCCGAG  U        AUU    GC     C    U         AG        ---UUU  U      UU
Stem-loop sequence	AGUCAUUGUUUGCUAUUGCAACAUCUUCAAGAUUCAGAAAUCAGAUUCUCUUAUGGGUUUUCUUUUGAGCCUUUAUUUUUUGGUUUGAGAAUCUUGAUGAUGCUGCAGCGGCAAUUAAAUGGCU

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
AY128328.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   ||||||||||||||=|||||| targets:520   CUGCAGCAUCAUCAGGAUUCU   540 Target Full Sequence	1.5	Arabidopsis thaliana APETALA2 protein (At4g36920) mRNA, complete cds	NA	coding protein	psRNATarget
U12546.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   ||||||||||||||=|||||| targets:1367   CUGCAGCAUCAUCAGGAUUCU   1387 Target Full Sequence	1.5	Arabidopsis thaliana Columbia homeotic APETALA2 protein (APETALA2) mRNA, complete cds	NA	coding protein	psRNATarget
NM_001204009.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   ||||||||||||||=|||||| targets:1293   CUGCAGCAUCAUCAGGAUUCU   1313 Target Full Sequence	1.5	Arabidopsis thaliana Integrase-type DNA-binding superfamily protein (AP2), mRNA	Integrase-type DNA-binding superfamily protein(AP2)	coding protein	psRNATarget
NM_119856.3	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   ||||||||||||||=|||||| targets:1452   CUGCAGCAUCAUCAGGAUUCU   1472 Target Full Sequence	1.5	Arabidopsis thaliana Integrase-type DNA-binding superfamily protein (AP2), mRNA	Integrase-type DNA-binding superfamily protein(AP2)	coding protein	psRNATarget
BT001916.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   *|||||||||||||=|||||| targets:1280   AUGCAGCAUCAUCAGGAUUCU   1300 Target Full Sequence	1.5	Arabidopsis thaliana clone C105157 putative APETALA2 protein (At5g60120) mRNA, complete cds	NA	coding protein	psRNATarget
AY074373.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   *|||||||||||||=|||||| targets:1643   AUGCAGCAUCAUCAGGAUUCU   1663 Target Full Sequence	1.5	Arabidopsis thaliana At5g60120 mRNA sequence	NA	coding protein	psRNATarget
NM_001345393.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   *|||||||||||||=|||||| targets:1723   AUGCAGCAUCAUCAGGAUUCU   1743 Target Full Sequence	1.5	Arabidopsis thaliana target of early activation tagged (EAT) 2 (TOE2), mRNA	target of early activation tagged (EAT) 2(TOE2)	coding protein	psRNATarget
NM_125405.4	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   *|||||||||||||=|||||| targets:1744   AUGCAGCAUCAUCAGGAUUCU   1764 Target Full Sequence	1.5	Arabidopsis thaliana target of early activation tagged (EAT) 2 (TOE2), mRNA	target of early activation tagged (EAT) 2(TOE2)	coding protein	psRNATarget
NM_001203647.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   *|||||||||||||=|||||| targets:1810   AUGCAGCAUCAUCAGGAUUCU   1830 Target Full Sequence	1.5	Arabidopsis thaliana target of early activation tagged (EAT) 2 (TOE2), mRNA	target of early activation tagged (EAT) 2(TOE2)	coding protein	psRNATarget
NM_001345392.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   *|||||||||||||=|||||| targets:1944   AUGCAGCAUCAUCAGGAUUCU   1964 Target Full Sequence	1.5	Arabidopsis thaliana target of early activation tagged (EAT) 2 (TOE2), mRNA	target of early activation tagged (EAT) 2(TOE2)	coding protein	psRNATarget
NM_001345391.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   *|||||||||||||=|||||| targets:2127   AUGCAGCAUCAUCAGGAUUCU   2147 Target Full Sequence	1.5	Arabidopsis thaliana target of early activation tagged (EAT) 2 (TOE2), mRNA	target of early activation tagged (EAT) 2(TOE2)	coding protein	psRNATarget
NM_001345390.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   *|||||||||||||=|||||| targets:1944   AUGCAGCAUCAUCAGGAUUCU   1964 Target Full Sequence	1.5	Arabidopsis thaliana target of early activation tagged (EAT) 2 (TOE2), mRNA	target of early activation tagged (EAT) 2(TOE2)	coding protein	psRNATarget
AF003100.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1127   CAGCAGCAUCAUCAGGAUUCU   1147 Target Full Sequence	1.5	Arabidopsis thaliana AP2 domain containing protein RAP2.7 mRNA, partial cds	NA	coding protein	psRNATarget
AF325074.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1265   CAGCAGCAUCAUCAGGAUUCU   1285 Target Full Sequence	1.5	Arabidopsis thaliana putative AP2 domain transcription factor (At2g28550) mRNA, complete cds	NA	coding protein	psRNATarget
AY091418.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1265   CAGCAGCAUCAUCAGGAUUCU   1285 Target Full Sequence	1.5	Arabidopsis thaliana putative AP2 domain transcription factor (At2g28550) mRNA, complete cds	NA	coding protein	psRNATarget
BX820052.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1544   CAGCAGCAUCAUCAGGAUUCU   1564 Target Full Sequence	1.5	Arabidopsis thaliana Full-length cDNA Complete sequence from clone GSLTLS68ZH07 of Adult vegetative tissue of strain col-0 of Arabidopsis thaliana (thale cress)	NA	coding protein	psRNATarget
BX820568.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1596   CAGCAGCAUCAUCAGGAUUCU   1616 Target Full Sequence	1.5	Arabidopsis thaliana Full-length cDNA Complete sequence from clone GSLTPGH48ZH11 of Hormone Treated Callus of strain col-0 of Arabidopsis thaliana (thale cress)	NA	coding protein	psRNATarget
AY050815.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1555   CAGCAGCAUCAUCAGGAUUCU   1575 Target Full Sequence	1.5	Arabidopsis thaliana putative AP2 domain transcription factor (At2g28550) mRNA, complete cds	NA	coding protein	psRNATarget
NM_001336171.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1780   CAGCAGCAUCAUCAGGAUUCU   1800 Target Full Sequence	1.5	Arabidopsis thaliana related to AP2.7 (RAP2.7), mRNA	related to AP2.7(RAP2.7)	coding protein	psRNATarget
NM_001336170.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1671   CAGCAGCAUCAUCAGGAUUCU   1691 Target Full Sequence	1.5	Arabidopsis thaliana related to AP2.7 (RAP2.7), mRNA	related to AP2.7(RAP2.7)	coding protein	psRNATarget
NM_128415.5	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1638   CAGCAGCAUCAUCAGGAUUCU   1658 Target Full Sequence	1.5	Arabidopsis thaliana related to AP2.7 (RAP2.7), mRNA	related to AP2.7(RAP2.7)	coding protein	psRNATarget
NM_001202696.2	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1683   CAGCAGCAUCAUCAGGAUUCU   1703 Target Full Sequence	1.5	Arabidopsis thaliana related to AP2.7 (RAP2.7), mRNA	related to AP2.7(RAP2.7)	coding protein	psRNATarget
NM_001336169.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1790   CAGCAGCAUCAUCAGGAUUCU   1810 Target Full Sequence	1.5	Arabidopsis thaliana related to AP2.7 (RAP2.7), mRNA	related to AP2.7(RAP2.7)	coding protein	psRNATarget
NM_001336168.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |*||||||||||||=|||||| targets:1896   CAGCAGCAUCAUCAGGAUUCU   1916 Target Full Sequence	1.5	Arabidopsis thaliana related to AP2.7 (RAP2.7), mRNA	related to AP2.7(RAP2.7)	coding protein	psRNATarget
BT029206.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   =*||||||||||||=|||||| targets:983   UGGCAGCAUCAUCAGGAUUCU   1003 Target Full Sequence	1.5	Arabidopsis thaliana At5g67180 mRNA, complete cds	NA	coding protein	psRNATarget
BX832834.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   =*||||||||||||=|||||| targets:1041   UGGCAGCAUCAUCAGGAUUCU   1061 Target Full Sequence	1.5	Arabidopsis thaliana Full-length cDNA Complete sequence from clone GSLTSIL15ZF12 of Silique of strain col-0 of Arabidopsis thaliana (thale cress)	NA	coding protein	psRNATarget
AY088238.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   =*||||||||||||=|||||| targets:1069   UGGCAGCAUCAUCAGGAUUCU   1089 Target Full Sequence	1.5	Arabidopsis thaliana clone 4623 mRNA, complete sequence	NA	coding protein	psRNATarget
NM_126118.4	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   =*||||||||||||=|||||| targets:1298   UGGCAGCAUCAUCAGGAUUCU   1318 Target Full Sequence	1.5	Arabidopsis thaliana target of early activation tagged (EAT) 3 (TOE3), mRNA	target of early activation tagged (EAT) 3(TOE3)	coding protein	psRNATarget
AK176145.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   =*||||||||||||=|||||| targets:1298   UGGCAGCAUCAUCAGGAUUCU   1318 Target Full Sequence	1.5	Arabidopsis thaliana mRNA for floral homeotic protein apetala2-like, complete cds, clone: RAFL22-96-G17	NA	coding protein	psRNATarget
JA894829.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   =||*||||||||||||||||* targets:16   UUGGAGCAUCAUCAAGAUUCA   36 Target Full Sequence	2.0	Sequence 146 from Patent WO2011067745	NA	coding protein	psRNATarget
AY576275.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   =|||||||||||||=|||||* targets:965   UUGCAGCAUCAUCAGGAUUCC   985 Target Full Sequence	2.5	Arabidopsis thaliana AP2 domain transcription factor (SMZ) mRNA, complete cds	NA	coding protein	psRNATarget
NM_115356.2	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   =|||||||||||||=|||||* targets:965   UUGCAGCAUCAUCAGGAUUCC   985 Target Full Sequence	2.5	Arabidopsis thaliana Integrase-type DNA-binding superfamily protein (SMZ), partial mRNA	Integrase-type DNA-binding superfamily protein(SMZ)	coding protein	psRNATarget
AK118705.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |||==|||||||||||||||* targets:592   CUGUGGCAUCAUCAAGAUUCA   612 Target Full Sequence	3.0	Arabidopsis thaliana mRNA for unknown protein, complete cds, clone: RAFL21-01-E23	NA	coding protein	psRNATarget
BX820161.1	ncRNA:21   GACGUCGUAGUAGUUCUAAGA   1   |||==|||||||||||||||* targets:586   CUGUGGCAUCAUCAAGAUUCA   606 Target Full Sequence	3.0	Arabidopsis thaliana Full-length cDNA Complete sequence from clone GSLTLS83ZF07 of Adult vegetative tissue of strain col-0 of Arabidopsis thaliana (thale cress)	NA	coding protein	psRNATarget

Reference

1	PMID:15200956 "Computational identification of plant microRNAs and their targets, including a stress-induced miRNA"; Jones-Rhoades MW, Bartel DP; Mol Cell. 14:787-799(2004).
2	PMID:16040653 "Expression of Arabidopsis MIRNA genes"; Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC; Plant Physiol. 138:2145-2154(2005).
3	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).
4	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).
5	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).