Stem-loop sequence cin-mir-141

Accession

MI0007168 (change log)

Description

Ciona intestinalis miR-141 stem-loop

Gene family

MIPF0000019; mir-8

Stem-loop

   ----------u          gg   u       ug        
5'            gguguaucuu  uca auagugu  uagauuc 
              ||||||||||  ||| |||||||  |||||| a
3'            uuacguagaa  ggu ugucaca  aucuagu 
   cucugugcagc          au   c       --        

Deep sequencing

8977 reads, 2.75e+03 reads per million, 2 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (JGI2): scaffold_71: 128547-128621 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from cin-mir-141

• cin-mir-200: scaffold_71: 128174-128259 [+]
• cin-mir-3575: scaffold_71: 128186-128245 [-]
• cin-mir-141: scaffold_71: 128547-128621 [+]
• cin-mir-5611: scaffold_71: 128684-128755 [+]

Database links

• EntrezGene:mir141
• miRBase Tracker:MI0007168

Mature sequence cin-miR-141-5p

• Accession: MIMAT0015260
• Previous IDs: cin-miR-141*
• Sequence: 7 - aucuuggucauauaguguug - 26
• Deep sequencing: 930 reads, 2 experiments
• Evidence: experimental; Illumina [3]

Mature sequence cin-miR-141-3p

• Accession: MIMAT0006103
• Previous IDs: cin-miR-141
• Sequence: 40 - uaacacugucugguaaagaugc - 61
• Deep sequencing: 8047 reads, 2 experiments
• Evidence: experimental; Northern [1], Illumina [3]

References

1. PMID:18047675 "Computational prediction and experimental validation of Ciona intestinalis microRNA genes" Norden-Krichmar TM, Holtz J, Pasquinelli AE, Gaasterland T BMC Genomics. 8:445(2007).
2. PMID:18339653 "Altered miRNA repertoire in the simplified chordate, Oikopleura dioica" Fu X, Adamski M, Thompson EM Mol Biol Evol. 25:1067-1080(2008).
3. PMID:20370911 "miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data" Hendrix D, Levine M, Shi W Genome Biol. 11:R39(2010).