miRBase entry: ath-MIR398c

Stem-loop ath-MIR398c


Accession
MI0001019
Description
Arabidopsis thaliana ath-MIR398c precursor miRNA
Gene family
MIPF0000107; MIR398

Literature search
30 open access papers mention ath-MIR398c
(122 sentences)

Sequence

uggaucucgacAGGGUUGAUAUGAGAACACACgagcaaucaacggcuauaacgacgcuacgucauuguuacagcucucguuucaUGUGUUCUCAGGUCACCCCUGcugagcucuu
.(((.((((.(((((.((((.((((((((((((((........((((.((((((((...))))...)))).))))))))).....))))))))).)))).))))).)))).))).

Structure
u   u    a     U    A         -----     caaucaac    a    ---    c 
 gga cucg cAGGG UGAU UGAGAACAC     ACgag        ggcu uaac   gacg  
 ||| |||| ||||| |||| |||||||||     |||||        |||| ||||   |||| u
 ucu gagu GUCCC ACUG ACUCUUGUG     ugcuc        ucga auug   cugc  
u   c    c     C    G         Uacuu     --------    c    uua    a 


Annotation confidence Not enough data
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Comments
This sequence belongs to the miR398 family of miRNAs, which are predicted to target mRNAs coding for copper superoxide dismutases and cytochrome C oxidase subunit V [1].

Genome context
chr5: 4694694-4694808 [+]
Clustered miRNAs
1 other miRNA is < 10 kb from ath-MIR398c
Name Accession Chromosome Start End Strand Confidence




Database links

Mature ath-miR398c-3p

Accession MIMAT0000950
Description Arabidopsis thaliana ath-miR398c-3p mature miRNA
Sequence 85 - UGUGUUCUCAGGUCACCCCUG - 105
Evidence experimental
5'RACE [1,3], Northern [1-2], PCR [1], cloned [2-3], 454 [4-5], MPSS [4]

Mature ath-miR398c-5p

Accession MIMAT0031912
Description Arabidopsis thaliana ath-miR398c-5p mature miRNA
Sequence 12 - AGGGUUGAUAUGAGAACACAC - 32
Evidence not_experimental

References

  1. PubMed ID: 16040653
    Expression of Arabidopsis MIRNA genes
    "Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC"
    "Plant Physiol (2005) 138:2145-2154

  2. PubMed ID: 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 (2006) 16:1276-1288

  3. PubMed ID: 17182867
    A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    "Rajagopalan R, Vaucheret H, Trejo J, Bartel DP"
    "Genes Dev (2006) 20:3407-3425

  4. PubMed ID: 15200956
    Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    "Jones-Rhoades MW, Bartel DP"
    "Mol Cell (2004) 14:787-799

  5. PubMed ID: 15258262
    Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
    "Sunkar R, Zhu JK"
    "Plant Cell (2004) 16:2001-2019