Table 2.

Non-coding RNAs in imprinted clusters in the mouse genome

Imprinted cluster (mouse chromosome)Macro ncRNAPublished sizeUnspliced or spliced/subcellular localisationCis-silencing functionHost for small RNAs
Igf2r (17) Airn1,* 108 kb2 95% unspliced (N) Yes4 Au76 siRNA5 

 

 

 
5% spliced to ∼1 kb (C)3
 

 

 
Kcnq1 (7)
 
Kcnq1ot16
 
∼90 kb7
 
Unspliced7,8(N)9,
 
Yes8,10
 

 
Pws/As (7) Snrpnlt(Lncat)11
 
Numerous splice variants11-13 Spliced11-13
 
n.d.
 
 
  Genomic size: 1000 kb11
 
Might contain all ncRNAs listed below
 
 Snord64 MBII-1314,15 
 Snurf U exons11
 
n.d.
 
n.d.
 
n.d.
 
Snord115 MBII-5214,15 
 Pwcr118
 
2.2 kb18
 
Unspliced18
 
n.d.
 
Snord116 MBII-8516,17 
 Ipw19
 
0.5-12 kb19 Several splice variants19 n.d.  
 
 
Genomic size: 60 kb
 
mainly(N)13,§
 

 
 
 Ube3a-ats20 n.d. Spliced/unspliced n.d. n.d.  

 

 

 
mainly(N)13,§
 

 

 
Gnas (2) Nespas21 Unspliced at least 3.35 kb22 Several spliced and unspliced versions22-24 n.d. mmu-mir-29625 
  Spliced 1.4-15.8 kb22,23   mmu-mir-29825 
 
 
Genomic size: at least 30 kb23
 

 

 

 
 Exon1A26 Unspliced >1.1 kb23 Spliced and unspliced23,26 n.d.  
  Spliced >1.4 kb26    

 

 
Genomic size: 19 kb
 

 

 

 
Igf2 (7) H1927 2.2 kb28 Spliced28 (C)29 no30 mmu-mir-67531 
 
 
Genomic size: 2.5 kb
 

 

 

 
 Igf2as32 4.8 kb32 Alternative promoters, spliced32
 
n.d.  

 

 
Genomic size: 10.7 kb
 
 
 

 
Dlk1 (12) Mico133
 
2 kb33
 
Unspliced33
 
n.d.
 
In silico predicted precursor miRNA33
 
 Mico1os33
 
2 kb33
 
Unspliced33
 
n.d.
 
In silico predicted precursor miRNA33
 
 Gtl2lt
 
Genomic size: 208 kb
 
Hypothetical transcript; might contain all ncRNAs listed below34-36
 
 mmu-mir: 770/673/493/337/540/665/431/433/1 27/434/136/341/1188/370/882/379/4 11/299/380/1197/323/758/329/494/6 79/1193/543/495/667/376c/654/376b/376a/300/381/487b/539/544/352/13 4/668/485/435/154/496/377/541/409/412/369/4134,37-40 
 Gtl243 1.9-7 kb43-45 Several splice variants43 n.d.  
 
 
Genomic size: 30.7 kb
 
mainly(N)43,§
 

 
 
 Rtl1as40
 
n.d.
 
Processed40
 
miRNAs involved in trans silencing of Rtl146
 
 
 Rian47 5.4 kb47 Spliced47 n.d. MBII-48(5), MBII-49(4), ImsnoRNA1, MBII-426(1), ImsnoRNA2, MBII-343(1),ImsnoRNA3, MBII-78(1), MBII-19(3)15,41,42 
 
 
Genomic size: 6.1 kb
 
mainly(N)47,
 

 
 
 Mirg40 1.3 kb40 Spliced40 n.d.  
  Genomic size: 14.5 kb    
Imprinted cluster (mouse chromosome)Macro ncRNAPublished sizeUnspliced or spliced/subcellular localisationCis-silencing functionHost for small RNAs
Igf2r (17) Airn1,* 108 kb2 95% unspliced (N) Yes4 Au76 siRNA5 

 

 

 
5% spliced to ∼1 kb (C)3
 

 

 
Kcnq1 (7)
 
Kcnq1ot16
 
∼90 kb7
 
Unspliced7,8(N)9,
 
Yes8,10
 

 
Pws/As (7) Snrpnlt(Lncat)11
 
Numerous splice variants11-13 Spliced11-13
 
n.d.
 
 
  Genomic size: 1000 kb11
 
Might contain all ncRNAs listed below
 
 Snord64 MBII-1314,15 
 Snurf U exons11
 
n.d.
 
n.d.
 
n.d.
 
Snord115 MBII-5214,15 
 Pwcr118
 
2.2 kb18
 
Unspliced18
 
n.d.
 
Snord116 MBII-8516,17 
 Ipw19
 
0.5-12 kb19 Several splice variants19 n.d.  
 
 
Genomic size: 60 kb
 
mainly(N)13,§
 

 
 
 Ube3a-ats20 n.d. Spliced/unspliced n.d. n.d.  

 

 

 
mainly(N)13,§
 

 

 
Gnas (2) Nespas21 Unspliced at least 3.35 kb22 Several spliced and unspliced versions22-24 n.d. mmu-mir-29625 
  Spliced 1.4-15.8 kb22,23   mmu-mir-29825 
 
 
Genomic size: at least 30 kb23
 

 

 

 
 Exon1A26 Unspliced >1.1 kb23 Spliced and unspliced23,26 n.d.  
  Spliced >1.4 kb26    

 

 
Genomic size: 19 kb
 

 

 

 
Igf2 (7) H1927 2.2 kb28 Spliced28 (C)29 no30 mmu-mir-67531 
 
 
Genomic size: 2.5 kb
 

 

 

 
 Igf2as32 4.8 kb32 Alternative promoters, spliced32
 
n.d.  

 

 
Genomic size: 10.7 kb
 
 
 

 
Dlk1 (12) Mico133
 
2 kb33
 
Unspliced33
 
n.d.
 
In silico predicted precursor miRNA33
 
 Mico1os33
 
2 kb33
 
Unspliced33
 
n.d.
 
In silico predicted precursor miRNA33
 
 Gtl2lt
 
Genomic size: 208 kb
 
Hypothetical transcript; might contain all ncRNAs listed below34-36
 
 mmu-mir: 770/673/493/337/540/665/431/433/1 27/434/136/341/1188/370/882/379/4 11/299/380/1197/323/758/329/494/6 79/1193/543/495/667/376c/654/376b/376a/300/381/487b/539/544/352/13 4/668/485/435/154/496/377/541/409/412/369/4134,37-40 
 Gtl243 1.9-7 kb43-45 Several splice variants43 n.d.  
 
 
Genomic size: 30.7 kb
 
mainly(N)43,§
 

 
 
 Rtl1as40
 
n.d.
 
Processed40
 
miRNAs involved in trans silencing of Rtl146
 
 
 Rian47 5.4 kb47 Spliced47 n.d. MBII-48(5), MBII-49(4), ImsnoRNA1, MBII-426(1), ImsnoRNA2, MBII-343(1),ImsnoRNA3, MBII-78(1), MBII-19(3)15,41,42 
 
 
Genomic size: 6.1 kb
 
mainly(N)47,
 

 
 
 Mirg40 1.3 kb40 Spliced40 n.d.  
  Genomic size: 14.5 kb    

This six well-studied imprinted clusters and their associated ncRNAs are listed with the macro ncRNA name, sizes of unspliced and spliced variants,genomic size if different from the longest unspliced version, and cellular localisation [note that nuclear localisation was sometimes inferred from RNA FISH (see Glossary, Box 1) data that did not exclude export to the cytoplasm]. Silencing function and hosted small ncRNAs are indicated. References: 1(Wutz et al.,1997), 2(Lyle et al., 2000), 3(Seidl et al., 2006), 4(Sleutels et al.,2002), 5(Watanabe et al., 2008), 6(Smilinich et al.,1999), 7(Pandey et al., 2008), 8(Mancini-Dinardo et al.,2006), 9(Terranova et al., 2008), 10(Shin et al.,2008), 11(Landers et al., 2004), 12(Gerard et al.,1999), 13(Le Meur et al., 2005), 14(Cavaille et al.,2000), 15(Huttenhofer et al.,2001), 16(Skryabin et al., 2007), 17(Ding et al.,2005), 18(de los Santos et al., 2000), 19(Wevrick and Francke,1997), 20(Chamberlain and Brannan,2001), 21(Wroe et al., 2000), 22(Williamson et al.,2002), 23(Holmes et al., 2003), 24(Li et al., 2000), 25(Royo et al.,2006), 26(Liu et al., 2000), 27(Pachnis et al.,1984), 28(Pachnis et al., 1988), 29(Brannan et al.,1990), 30(Schmidt et al., 1999), 31(Cai and Cullen,2007), 32(Moore et al., 1997), 33(Labialle et al.,2008), 34(Seitz et al., 2004), 35(da Rocha et al., 2008), 36(Tierling et al.,2006), 37(Lagos-Quintana et al.,2002), 38(Houbaviy et al., 2003), 39(Kim et al.,2004), 40(Seitz et al., 2003), 41(Cavaille et al.,2002), 42(Xiao et al., 2006), 43(Schuster-Gossler et al.,1998), 44(Schmidt et al., 2000), 45(Miyoshi et al.,2000), 46(Davis et al., 2005), 47(Hatada et al.,2001).

C, cytoplasmic; ImsnoRNA, snoRNAs at the Irm locus; MBII, mouse brain 2; mmu-mir, Mus musculus microRNA; N, nuclear; n.d., not determined.

*

Renamed from Air by HUGO nomenclature committee.

Provisional name.

By RNA FISH.

§

By whole-mount in situ hybridisation.

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