Stem-loop sequence ssc-mir-18a

Accession

MI0002455 (change log)

Previous IDs

ssc-mir-18

Description

Sus scrofa miR-18a stem-loop

Gene family

MIPF0000001; mir-17

Literature search

18 open access papers mention ssc-mir-18a
(50 sentences)

Stem-loop

   ---gu         u   --   u   uc   u    a   -  aa u 
5'      gcuuuuugu cua  agg gca  uag gcag uag ug  g a
        ||||||||| |||  ||| |||  ||| |||| ||| ||  | g
3'      ugaagaaua ggu  ucc cgu  auc cguc auc ac  u a
   uguau         c   cu   u   ga   c    -   u  ga u 

Deep sequencing

603 reads, 73.3 reads per million, 15 experiments

Confidence

Annotation confidence: not enough data

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Genome context

• Coordinates (Sscrofa10.2; GCA_000003025.4): chr11: 66610195-66610286 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from ssc-mir-18a

• ssc-mir-17: chr11: 66610060-66610136 [+]
• ssc-mir-18a: chr11: 66610195-66610286 [+]
• ssc-mir-19a: chr11: 66610343-66610424 [+]
• ssc-mir-20a: chr11: 66610513-66610583 [+]
• ssc-mir-19b-1: chr11: 66610642-66610721 [+]
• ssc-mir-92a-1: chr11: 66610762-66610841 [+]

Database links

• EntrezGene:MIR18
• miRBase Tracker:MI0002455

Mature sequence ssc-miR-18a

• Accession: MIMAT0002161
• Previous IDs: ssc-miR-18
• Sequence: 14 - uaaggugcaucuagugcagaua - 35
• Deep sequencing: 596 reads, 15 experiments
• Evidence: experimental; cloned [2], Illumina [3-4]

References

1. PMID:15885146 "Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing" Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L BMC Genomics. 6:70(2005).
2. PMID:20180025 "Cloning and characterization of microRNAs from porcine skeletal muscle and adipose tissue" Cho IS, Kim J, Seo HY, Lim DH, Hong JS, Park YH, Park DC, Hong KC, Whang KY, Lee YS Mol Biol Rep. 37:3567-3574(2010).
3. PMID:21312241 "MicroRNA identity and abundance in developing swine adipose tissue as determined by Solexa sequencing" Li G, Li Y, Li X, Ning X, Li M, Yang G J Cell Biochem. 112:1318-1328(2011).
4. PMID:24499489 "Exploration of microRNAs in porcine milk exosomes" Chen T, Xi QY, Ye RS, Cheng X, Qi QE, Wang SB, Shu G, Wang LN, Zhu XT, Jiang QY, Zhang YL BMC Genomics. 15:100(2014).