We searched for 2,563 microRNA (miRNA) binding sites in 17,494 mRNA sequences of human genes. miR-1322 has more than 2,000 binding sites in 1,058 genes with
Interest in microRNAs (miRNAs) is constantly growing, and new data supplement existing knowledge about the role of these molecules in key biological processes. The main objective of these studies is to identify miRNA binding sites and evaluate their binding affinities. The characteristics of binding sites shed light on the biological role of miRNAs and have practical applications. It is possible to predict interactions between miRNAs and mRNAs and their properties by using computational methods [
The nucleotide sequences of precursor mRNAs (pre-mRNAs) of human genes (
Target genes for miR-1322 were determined using the MirTarget program [
miR-1322 has a length of 19 nucleotides (nt) and a GC-content of 53%. The maximum free energy of miR-1322 binding with mRNAs is −101.9 kJ/mole. We found that miR-1322 has 2,264 binding sites on 1,058 target mRNAs with a
The maximum number of sites observed in 3′ UTR is eight in
Characteristics of miR-1322 binding sites located through three nucleotides in the CDSs of some mRNAs. The number of binding sites in the mRNA fragment is indicated within parentheses.
Gene | Position of binding sites, nt |
|
Oligopeptide |
---|---|---|---|
|
1471–1486 (6) | 85.4 ÷ 87.5 | SSSSSSSGSSS |
|
1286–1334 (17) | 87.5 | QQQQQQQQQQQQQQQQQQQQQQ |
|
213–225 (5) | 87.5 | QQQQQQQQQQ |
|
724–742 (8) | 87.5 | QQQQQQQQQQQA |
|
1692–1731 (13) | 87.5 ÷ 91.7 | QQQQQQQQQQQQQQQQQH |
|
1559–1592 (12) | 85.4 ÷ 91.7 | QQQQQQQQQQQQHQHQQ |
1604–1631 (10) | 87.5 ÷ 89.6 | QQQQQQQQQQQQQQH | |
|
657–684 (10) | 87.5 | QQQQQQQQQQQQQQQ |
699–714 (6) | 87.5 ÷ 89.6 | QQQQQQQQQPР | |
|
637–658 (8) | 85.4 ÷ 89.6 | QQQQQPPPPQPQ |
|
763–775 (5) | 85.4 ÷ 87.5 | SSSSSSSSSS |
|
1224–1236 (5) | 85.4 ÷ 87.5 | GSSSSSSSSS |
|
1543–1555 (5) | 87.5 | QQQQQQQQQQ |
1600–1615 (6) | 85.4 ÷ 91.7 | QQQQQQQQHHH | |
|
1283–1298 (6) | 85.4 ÷ 87.5 | QQQRQQQQQQQ |
|
1871–1883 (5) | 87.5 | QQQQQQQQQQ |
|
980–1007 (10) | 85.4 ÷ 87.5 | SSSSSSSSSSSSSNS |
|
8333–8363 (11) | 87.5 | QQQQQQQQQQQQQQQQ |
|
732–753 (8) | 85.4 ÷ 87.5 | QQQQRQQQQQQQ |
|
408–432 (9) | 87.5 | QQQQQQQQQQQQQQ |
|
414–435 (8) | 85.4 ÷ 87.5 | RQQQQQQQQQQQ |
|
196–247 (19) | 85.4 ÷ 89.6 | QQQQQQQQQQQQQQQQQQQQQQQ |
|
1249–1267 (7) | 87.5 | QQQQQQQQQQQQ |
|
2088–2100 (5) | 85.4 ÷ 87.5 | SSSSSSSNAV |
|
512–539 (10) | 87.5 ÷ 91.7 | QQQQQQQQQQQQQQP |
|
4794–4815 (8) | 87.5 | QQQQQQQQQQQQQ |
|
1759–1771 (5) | 87.5 | QQQQQQQQQQ |
|
3064–3091 (10) | 87.5 | QQQQQQQQQQQQQQQ |
|
2219–2264 (16) | 87.5 | QQQQQQQQQQQQQQQQQQHSN |
2678–2690 (5) | 87.5 ÷ 91.7 | QQQQQPPPPQ | |
|
710–722 (5) | 87.5 ÷ 91.7 | QQQQQQQQHL |
830–848 (7) | 87.5 | QQQQQQQQQQQQ | |
|
1836–1860 (9) | 85.4 ÷ 89.6 | GFQQQQQQQQQQQP |
|
729–741 (5) | 85.4 ÷ 87.5 | SSSSSSSSSS |
762–774 (5) | 85.4 ÷ 87.5 | SSSSSSSSSS | |
|
2524–2539 (6) | 87.5 | QQQQQQQQQQQ |
|
622–643 (8) | 87.5 ÷ 91.7 | SSSSSSSSSSSIP |
|
549–561 (5) | 85.4 ÷ 87.5 | GSGSSSSSSG |
|
4023–4038 (6) | 87.5 | QQQQQQQQQQQ |
|
1126–1138 (5) | 87.5 | QQQQQQQQQQ |
|
1812–1830 (7) | 87.5 ÷ 91.7 | QQQQQQQQQQQQ |
|
408–429 (8) | 85.4 ÷ 87.5 | QQQQQQQQQQQQQ |
|
701–719 (7) | 85.4 ÷ 89.6 | QQQQQQQQQQPP |
|
785–797 (5) | 85.4 | AAAAAAAAAA |
|
1300–1324 (9) | 87.5 | QQQQQQQQQQQQQQ |
|
590–602 (5) | 85.4 ÷ 87.5 | SSSSSSSSSG |
|
3303–3315 (5) | 87.5 ÷ 91.7 | QQQQQQQPPP |
|
765–795 (11) | 87.5 | QQQQQQQQQQQQQQQQ |
|
394–406 (5) | 87.5 ÷ 91.7 | AAAAAAAAAP |
|
468–480 (5) | 87.5 | QQQQQQQQQQ |
501–546 (16) | 87.5 | QQQQQQQQQQQQQQQQQQQQQ | |
|
611–629 (7) | 87.5 ÷ 91.7 | QQQQQQQQQQQQ |
|
2348–2363 (6) | 87.5 ÷ 91.7 | QQQQQQQQQPR |
|
1151–1175 (9) | 87.5 | TSNQKQQQQQQQQQ |
|
1770–1806 (13) | 87.5 ÷ 91.7 | QQQQQQQQQQQQQQQQPP |
The arranged nucleotide sequences of the CDSs contain binding sites for miR-1322 (Figure
The arrangement of miR-1322 binding sites in CDSs of human target genes.
Nucleotide variation in the miR-1322 binding sites in the CDSs of human target genes.
The
The arrangement of miR-1322 binding sites in 5′ UTRs and 3′ UTRs human target genes.
Gene | Position of binding sites, nt |
|
---|---|---|
|
25–43 (7) | 85.4 ÷ 87.5 |
|
7170–7191 (8) | 87.5 |
|
118–136 (7) | 85.4 ÷ 87.5 |
|
178–199 (8) | 87.5 ÷ 89.6 |
|
53–86 (12) | 85.4 ÷ 89.6 |
|
342–378 (13) | 87.5 |
|
1413–1425 (5) | 85.4 ÷ 87.5 |
|
103–118 (7) | 85.4 ÷ 89.6 |
|
323–335 (5) | 87.5 ÷ 91.7 |
Note: the symbol “*” indicates binding site localization in the 3′ UTR.
Transcription factors represent 33% of all target genes in this study (Figure
The relationship between paralogous and orthologous mRNAs of the
Various paralogous genes are targets for miR-1322. Two regions contain multiple miR-1322 binding sites in
Conserved amino acid sequences containing polyglutamine in orthologous
The number of amino acids in orthologous proteins depends on the species (Figure
miR-1322 binding sites in orthologous
Conserved amino acid sequences containing polyglutamine in orthologous
Conserved amino acid sequences containing polyglutamine in orthologous
The CDS of the human
The CDS of the human
The presence of multiple miR-1322 binding sites in
The glutamine-containing regions play an important role in the development of different diseases, according to previous literature. It is possible that changes in the dependence of the interactions between miR-1322 and
The authors declare that there is no conflict of interests regarding the publication of this paper.