Stem-loop sequence ssc-mir-500

Accession

MI0013166 (change log)

Description

Sus scrofa miR-500 stem-loop

Gene family

MIPF0000139; mir-500

Literature search

3 open access papers mention ssc-mir-500
(7 sentences)

Stem-loop

   ----ccc     -u         uac ug    agag   ugu 
5'        cucuc  aauccuugc   c  ggug    ugc   g
          |||||  |||||||||   |  ||||    |||   u
3'        gagag  uuaggaacg   g  ccac    acg   g
   cgagagu     uc         --- gu    -gua   uaa 

Deep sequencing

1232 reads, 20 reads per million, 15 experiments

Confidence

Annotation confidence: high

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Genome context

• Coordinates (Sscrofa10.2; GCA_000003025.4): chrX: 48637994-48638073 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from ssc-mir-500

• ssc-mir-532: chrX: 48632025-48632104 [+]
• ssc-mir-500: chrX: 48637994-48638073 [+]
• ssc-mir-362: chrX: 48638466-48638544 [+]
• ssc-mir-660: chrX: 48640821-48640889 [+]

Database links

• EntrezGene:MIR500
• miRBase Tracker:MI0013166

Mature sequence ssc-miR-500-5p

• Accession: MIMAT0037369
• Sequence: 9 - uaauccuugcuaccugggugaga - 31
• Deep sequencing: 317 reads, 15 experiments
• Evidence: experimental; Illumina [4]

Mature sequence ssc-miR-500-3p

• Accession: MIMAT0013956
• Sequence: 48 - augcaccugggcaaggauucu - 68
• Deep sequencing: 915 reads, 15 experiments
• Evidence: experimental; Illumina [1,3], cloned [2]

References

1. 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).
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: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).
4. PMID:25230983 "The characteristics of the porcine (Sus scrofa) liver miRNAome with the use of next generation sequencing" Pawlina K, Gurgul A, Oczkowicz M, Bugno-Poniewierska M J Appl Genet. 56:239-252(2015).