Stem-loop sequence ssc-mir-17

Accession

MI0008214 (change log)

Description

Sus scrofa miR-17 stem-loop

Gene family

MIPF0000001; mir-17

Literature search

30 open access papers mention ssc-mir-17
(81 sentences)

Stem-loop

   ga       -ca        a  g     g   -  aua 
5'   auaaugu   aagugcuu ca ugcag uag ug   a
     |||||||   |||||||| || ||||| ||| ||    
3'   uauuacg   uucacgga gu acguc auc ac   u
   gg       aug        a  g     -   u  gug 

Deep sequencing

5108 reads, 647 reads per million, 15 experiments

Confidence

Annotation confidence: not enough data

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Genome context

• Coordinates (Sscrofa10.2; GCA_000003025.4): chr11: 66610060-66610136 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from ssc-mir-17

• 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:MIR17
• miRBase Tracker:MI0008214

Mature sequence ssc-miR-17-5p

• Accession: MIMAT0007755
• Previous IDs: ssc-miR-17
• Sequence: 10 - caaagugcuuacagugcagguag - 32
• Deep sequencing: 4969 reads, 15 experiments
• Evidence: experimental; cloned [1,3], Illumina [2,4-5]

Mature sequence ssc-miR-17-3p

• Accession: MIMAT0015268
• Sequence: 48 - acugcagugaaggcacuuguag - 69
• Deep sequencing: 139 reads, 14 experiments
• Evidence: experimental; Illumina [2,4-5]

References

1. PMID:18548309 "Identification and characterization of new microRNAs from pig" Kim J, Cho IS, Hong JS, Choi YK, Kim H, Lee YS Mamm Genome. 19:570-580(2008).
2. PMID:19917043 "MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing" Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C, Thomsen B Anim Genet. 41:159-168(2010).
3. 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).
4. 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).
5. 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).