Non-coding RNAs in imprinted clusters in the mouse genome
Imprinted cluster (mouse chromosome) . | Macro ncRNA . | Published size . | Unspliced or spliced/subcellular localisation . | Cis-silencing function . | Host 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 ncRNA . | Published size . | Unspliced or spliced/subcellular localisation . | Cis-silencing function . | Host 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.