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Table 1 List of snoRNA/scaRNA candidates

From: Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana

IDa Coordinatesb Type Putative target Copies (TeloSII)c cDNA/EST RNA-Seq Tissue Homologyd
Cluster1 ncR1 Chr1:14283553..14283663 H/ACA / 9(1) / GSM893120 flowers A.ly
ncR2 Chr1:14283835..14283886 C/D / 4(1) / / / /
ncR3 Chr1:14283975..14284049 C/D 18S/Am1750 (D) 5(1) / GSM442932 roots /
ncR4 Chr1:14284343..14284424 C/D 18S/Cm307 (D) 2(1) / GSM575247 flowers A.ly
Cluster2 ncR5 Chr2:1836965..1837036 C/D 25S/Cm2509 (D) 1 / GSM893122 flowers A.ly
ncR6 Chr2:1837308..1837401 C/D 18S/Gm275 (D) 1 / GSM893120 flowers A.ly
ncR7 Chr2:1837461..1837557 C/D U2.4/Gm331 (D) 12(1) / GSM893120 flowers A.ly
Cluster3 ncR9 Chr2:5830603..5830668 C/D U5/Tm687 (D) 2(1) / GSM893122 flowers Cru
ncR10 Chr2:5831355..5831456 C/D U6.29/Cm590 (D) 4(1) / GSM893123 flowers A.ly
Cluster4 ncR11 Chr4:1480138..1480215 C/D 25S/Cm2616 (D) 1 / GSM893120 flowers A.ly, C.ru
ncR12 Chr4:1480326..1480415 C/D U4.1/Am223 (D) 1 / GSM893121 flowers A.ly
Cluster5 ncR13 Chr5:3642290..3642331 C/D U6.29/Am296 (D') 1 / / / /
ncR14 Chr5:3642496..3642628 C/D U6.26/Um774 (D) 1 / SRR505744 leaves A.ly, C.ru, B.ra
Cluster6 ncR15 Chr5:20313629..20313716 C/D / 1 / GSM893122 flowers /
ncR16 Chr5:20313841..20313928 C/D / 1 / GSM893123 flowers A.ly
ncR17 Chr5:20314434..20314506 C/D U5/Am921 (D) 1 / GSM893121 flowers A.ly
Cluster7 ncR20 Chr2:9809815..9809713 C/D U6-29/Am21 (D) 1 EH971193 SRR505743 seedlings, roots A.ly
ncR21 Chr2:9809455..9809345 C/D U2.4/Cm143 (D) 1 / SRR505745 flowers A.ly, C.ru
Cluster8 ncR22 Chr4:5918068..5917991 C/D U2.3/Am345 (D) 8(6) / GSM893121 flowers A.ly
ncR23 Chr4:5917772..5917612 C/D U2.9/Tm207 (D) 12(4) / GSM456944 flowers A.ly
Cluster9 ncR24 Chr5:10673349..10673223 H/ACA / 1 / GSM893122 flowers A.ly
ncR25 Chr5:10672936..10672800 H/ACA / 11(2) / GSM893121 flowers A.ly
Cluster10 ncR26 Chr1:28889830..28889897 C/D U6.1/Cm740 (D) 1 / GSM896913 leaves A.ly, Cru, B.ra
ncR27 * Chr1:28889966..28890048 C/D U6.1/Am177 (D) 1 / GSM896913 flowers A.ly, Cru
Single ncR18 Chr1:26010695..26010627 C/D 18S/Am1558 (D) 1 / / / A.ly
Single ncR28 Chr1:6140665..6140735 C/D 18S/Gm727 (D) 1 / GSM893122 flowers /
  1. aID with triangle was also identified as long ncRNA by Liu et al. [38]. ID with asterisk was also identified as intermediate ncRNA by Wang et al. [39]. ID marked in bold was verified by RT-PCR in this study
  2. bTermini were predicted by snoReport program, and fine-turned based on small RNA enrichments and RT-PCR validation
  3. cNumbers within parentheses denote copies also containing TeloSII elements
  4. dConservation analysis were performed in Arabidopsis lyrata (A.ly), Capsella rubella (C.ru), Brassica rapa (B.ra), Medicago truncatula (M.tr) and Oryza sativa (O.sa)