Table 6 Putative polymorphisms identified at miRNA target sites and inside miRNA mature sequences
From: A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.)
miRNA family | miRNA name | Unigene | Unigene cluster annotation | Putative Polymorphisms at miRNA target site (5'-3') | Barley miRNA mature sequence (5'-3') |
|---|---|---|---|---|---|
156 | miR156 | Hv.5875 | protein coding (SBP domain) | #GTGCTCTCT(C)CTCTTCTGTCA | UGACAGAAGAGA GAGAGCAC (12) |
| Â | miR156 | Hv.21387 | SPL2 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2) | #ATGCTCTC(G)TC(T)TC(G)TTCTGTCA | UGACAGAAG AG AG AGAGCAU (9-11-13) |
164 | miR164 | Hv.28795 | NAC domain containing protein | #AGCAAGTGCCC(A)TGCTTCTCCA | UGGAGAAGCAG GGCACUUGCU (11) |
169 | miR169 | Hv.13681 | CCAAT-binding transcription factor (CBF-B/NF-YA) family protein | #CAGGCAACTCATCCTTGGCT(C)T | AA GCCAAGGAUGAGUUGCCUG (2) |
| Â | miR169 | Hv.9532 | CCAAT-binding transcription factor (CBF-B/NF-YA) family protein | #GGCAATTCATCCTTGGC(T)TT | AAG CCAAGGAUGAAUUGCC (3) |
393 | miR393 | Hv.2498 | TIR1 (TRANSPORT INHIBITOR RESPONSE 1), ubiquitin-protein ligase | #G(C)ACAATGCG(T)ATCCC(+CT)TTTGGA | UCCAAA() GGGAUC GCAUUGUC (6-12-20) |
396 | miR396 | Hv.9742 | WRC, QLQ | #GTTCAAG(A)AAAGCCTGTGGA | UCCACAGGCUUUC UUGAAC(13) |
408 | miR408 | Hv.20945 | ARGONAUTE like superfamily | #CAGGGCAG(T)AGGCAGTGCAG | CUGCACUGCCUC UGCCCUG (12) |
| Â | miR408 | AutoSNP contig 2094 | Plastocyanin | #CAGGGAAGAGGCA(C) GTGCGG | CCGCACU(G) GCCUCUUCCCUG (7) |
444 | miR444 | Hv.16297 | / | Â | *GCAGUUGCU(C) GCCUCAAGCUU (9) |
818 | miR818 | Hv.11323 | protein coding | #CCGTCCCATAA(CC)TATAAGGG | CCCUUAUAU UAUGGGACGG (9) |
| Â | miR1436 | Hv.8351 | protein coding | #ACTCCCTCC(T) GTCCCATAAT | AUUAUGGGACG GAGGGAGU (11) |
| Â | miR1436 | Hv.11323 | protein coding | #ACTCCCTCCGTCCCATAA--(CC)T | A-- UUAUGGGACGGAGGGAGU (2) |
| Â | miR1439 | Hv.23816 | exo-endo-phos superfamily | # AATACTCACTCCGTCCCAAAA(G) | U UUUGGGACGGAGUGAGUAUU (1) |
| Â | miR1439 | Hv.11224 | tatD-related deoxyribonuclease family protein | #TACTCACTCCGTTCCA(T) AAA | UUUU GGAACGGAGUGAGUA (4) |
821 | miR821 | Hv.3660 | GDH1 (Glutamate dehydrogenase) | #TCAA(C)CAAAAAAGTTGAAT | AUUCAACUUUUUUGU UGA (15) |
1030 | miR1030 | Hv.14867 | RNA recognition motif (RRM)-containing protein | #TGGT(G)GCAGGTGCAGGTGCAGG | CCUGCACCUGCACCUGCA CCA (18) |
1119 | miR1119 | Hv.29226 | / | Â | *UGGC(-)A(C)CGGCGCGAUGCUCAGUCA(-)G(C) (4-5-23-24) |
| Â | miR1119 | Hv.29225 | protein coding | #CTGAC(A)TGAGCATCGCGCCGTGCCA | UGGCACGGCGCGAUGCUCAG UCAG (20) |
| Â | miR1119 | Hv.27666 | protein coding | #C(T)TGAC(T/A)TG(A)A(G)GCA(T)TCGCGCCGTGCC | GGCACGGCGCGAU GCUC AG UCAG (13-16-17-19-23) |
| Â | miR1119 | Hv.23343 | molybdenum cofactor sulfurase family protein, superfamily | #CT(G)G(T)A(G) CT(C) GAGCATCGCGCCGTGCC | GGCACGGCGCGAUGCUCA GUCA G (18-20-21-22) |
| Â | miR1119 | Hv.29210 | protein coding | #T(G)GGCACG(A)GC(T)GCGAT(A)GCTCAG(A)TCAG(A) | C UGAC UGAGCA UCGCG CC GUGCCA (1-5-11-16-18-24) |
1120 | miR1121 | Hv.464 | serine/threonine kinase | #A(G)A(G)GAGCGTTTAGATCACTA | UAGUGAUCUAAACGCUCUU (18-19) |
| Â | miR1121 | Hv.6581 | protein coding | #TAAGAGCGTTTAGATCACT(C) A | UA GUGAUCUAAACGCUCUUA (2) |
| Â | miR1121 | Hv.6532 | ATPase-Plipid, haloacid dehalogenase-like hydrolase family protein | #TAAG(A)AGTGTTTAGATCACTACT | AGUAGUGAUCUAAACACUC UUA (19) |
| Â | miR1121 | Hv.5064 | / | Â | *UAGUACAAAGUUG(C)AGUCA (13) |
1122 | miR1128 | Hv.14876 | ARF-GAP DOMAIN, C2 superfamily | #TTTG(T)GG(A)ACGGA(G)GGGAGTAGTA | UACUACUCCCU CCGUC CC AAA (11-16-18) |
| Â | miR1133 | Hv.12091 | oxidoreductase, zinc-binding dehydrogenase family protein | #TTTGGG(A)ACGGAGGGAGTAC(-)TAT | AUAG UACUCCCUCCGUC CCAAA (3-16) |
| Â | miR1133 | Hv.28555 | serine/threonine protein kinase, PKc-like superfamily | #TTTCGGACAGAGGG(T)AGTATAT | AUAUACUC CCUCUGUCCGAAA (8) |
| Â | miR1135 | Hv.18515 | ubiquitin family protein | #TTC(G)GGAATTACTTGTCGCA | UGCGACAAGUAAUUCCG AA (17) |
1134 | miR1134 | Hv.22973 | octopine synthase binding factor1, ATBZIP53 (BASIC REGION/LEUCINE ZIPPER MOTIF 53), DNA binding/protein heterodimerization/sequence-specific DNA binding/transcription factor | #TCTTCTTCTTCTTCTTG(C)TTC(---) TTG | CAAGAAC AAGAAGAAGAAGAAGA (4-5-6-7) |
| Â | miR1134 | Hv.9579 | L-asparaginase, putative/L-asparagine amidohydrolase, putative | #TC(G)T(C) TCTTCTTCTTGGTGTTGGTG | CACCAACACCAAGAAGAAGAAG A (21-22) |
| Â | miR1134 | Hv.26138 | AWPM-19-like membrane family protein | #TCTTCTTC(G)TTCTT(A)GTCGTTGTTG | CAACAACGACA AGAAG AAGAAGA (11-16) |
| Â | miR1134 | Hv.24001 | dehydrin family protein | #TTCTTCTTCTTGTTGTTTTT(-) G | CA AAAACAACAAGAAGAAGAA (2) |
| Â | miR1134 | Hv.8025 | / | Â | *UCUUCUUCUUUUGUUGUUGU(C)UG (20) |
| Â | miR1134 | Hv.5763 | / | Â | *CUUC(G) UUCCUCUUGUUGUUGUUG (4) |
1871 | miR1871 | Hv.28885 | protein coding | # C(T) AACATGATATCAGAGCCA | UGGCUCUGAUAUCAUGUUG (19) |