Stem-loop sequence kshv-miR-K12-2

Accession

MI0002476 (change log)

Description

Kaposi sarcoma-associated herpesvirus miR-K12-2 stem-loop

Stem-loop

     -   u   u  c  a  g      g  uc      agccauu    c 
5' gg guc acu cg ua cu uagucc gg  gaucug       gaag a
   || ||| ||| || || || |||||| ||  ||||||       ||||  
3' cc cag ugg gc gu ga aucggg cc  cuagac       cuuc a
     a   -   c  c  c  g      a  uu      -------    g 

Confidence

Annotation confidence: not enough data

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Comments

Cai et al. define the likely miRNA primary transcripts in [2].

Genome context

• Coordinates (EMBL:U75698.1): KSU75698: 121674-121764 [-]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from kshv-miR-K12-2

• kshv-mir-K12-1: KSU75698: 121847-121913 [-]
• kshv-miR-K12-2: KSU75698: 121674-121764 [-]
• kshv-mir-K12-3: KSU75698: 121544-121613 [-]
• kshv-mir-K12-4: KSU75698: 121413-121482 [-]
• kshv-mir-K12-5: KSU75698: 121263-121332 [-]
• kshv-mir-K12-6: KSU75698: 120761-120822 [-]
• kshv-mir-K12-11: KSU75698: 120576-120646 [-]
• kshv-mir-K12-7: KSU75698: 120355-120426 [-]
• kshv-mir-K12-8: KSU75698: 119943-120012 [-]
• kshv-mir-K12-9: KSU75698: 119300-119365 [-]
• kshv-mir-K12-10a: KSU75698: 117967-118036 [-]
• kshv-mir-K12-12: KSU75698: 117674-117771 [-]

Database links

• miRBase Tracker:MI0002476

Mature sequence kshv-miR-K12-2-5p

• Accession: MIMAT0002183
• Previous IDs: kshv-miR-K12-2
• Sequence: 15 - aacuguaguccgggucgaucug - 36
• Evidence: experimental; cloned [1], Illumina [3], SOLiD [4]

Mature sequence kshv-miR-K12-2-3p

• Accession: MIMAT0015215
• Previous IDs: kshv-miR-K12-2*
• Sequence: 58 - gaucuuccagggcuagagcug - 78
• Evidence: experimental; Illumina [3], SOLiD [4]

References

1. PMID:15800047 "Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells" Cai X, Lu S, Zhang Z, Gonzalez CM, Damania B, Cullen BR Proc Natl Acad Sci U S A. 102:5570-5575(2005).
2. PMID:16474131 "Transcriptional origin of Kaposi's sarcoma-associated herpesvirus microRNAs" Cai X, Cullen BR J Virol. 80:2234-2242(2006).
3. PMID:19889781 "In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery" Umbach JL, Cullen BR J Virol. 84:695-703(2010).
4. PMID:20566670 "Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs" Lin YT, Kincaid RP, Arasappan D, Dowd SE, Hunicke-Smith SP, Sullivan CS RNA. 16:1540-1558(2010).