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Table 3 Putative miRNA-mRNA interactions. The possible miRNA-mRNA interactions are listed for the DE-miRNAs and for other miRNAs of interests. Bolded hits represent interactions involving DEGs. The gene IDs and putative annotations are reported according to the oyster genome annotation (v.9) and the IDs without annotation refer to proteins with unknown function (annotated as “hypothetical protein”). The underlined match to Histone deacetylase 6) refers to a miRNA-mRNA interaction described also in humans

From: Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1

miRNA ID 3′-UTR matches
DE-miRNAs Gene ID (functional annotation)
Cgi-Mir-10-P5 CGI_10021820, CGI_10022274 (Chloride channel protein 7), CGI_10022274, CGI_10022383 (Universal stress protein A-like protein), CGI_10026565 (Homeobox protein Hox-B7)
Cgi-Mir-12 CGI_10006175 (Lipoma HMGIC fusion partner-like 3 protein), CGI_10006175, CGI_10020896 (Vitamin D3 receptor A)
Cgi-Mir-133-v1 CGI_10000616 (Laminin subunit beta-2), CGI_10015881 (Calcium-dependent protein kinase 31), CGI_10015881, CGI_10015881, CGI_10016880 (Collagen alpha-1(XIV) chain)
Cgi-Mir-133-v2 CGI_10001808 (26S protease regulatory subunit 7), CGI_10021971, CGI_10021971, CGI_10022309
Cgi-Mir-193-P1 CGI_10014060
Cgi-Mir-1985 CGI_10000475 (Aldose 1-epimerase), CGI_10016699 (Hexosaminidase domain-containing protein), CGI_10016780 (Spindle and kinetochore-associated protein 2), CGI_10017457 (Endo-1,6-beta-D-glucanase BGN16.3), CGI_10017496 (Kinesin-associated protein 3), CGI_10021840 (Kelch-like protein 20), CGI_10026811 (Inositol hexakisphosphate kinase 1), CGI_10027003 (Proteasome subunit beta type-3)
Cgi-Mir-1993 CGI_10021960 (Ras-related protein Rab-3), CGI_10021960, CGI_10021960
Cgi-Mir-216-P1 CGI_10017498 (Glycosyltransferase 25 family member 1), CGI_10017964 (Histone deacetylase 6), CGI_10020367 (Prostaglandin E2 receptor EP4 subtype), CGI_10021263 (Serine)
Cgi-Mir-315-v1 CGI_10000496, CGI_10016596 (Sacsin), CGI_10021927 (GTP-binding protein REM 1), CGI_10022452 (Small nuclear ribonucleoprotein E)
Cgi-Mir-315-v2 CGI_10000496, CGI_10009680 (Casein kinase II subunit alpha), CGI_10016245 (Rhophilin-2-B), CGI_10016506 (24-hydroxycholesterol 7-alpha-hydroxylase), CGI_10016596, CGI_10021971 (Myosin regulatory light chain sqh), CGI_10021971, CGI_10022309 (N-acetyltransferase 11)
Cgi-Mir-375-P4 CGI_10009294, CGI_10009754 (Histone-lysine N-methyltransferase, H3 lysine-9specific 3), CGI_10016585 (Calmodulin-like protein 11), CGI_10017336 (FERM domain-containing protein 1), CGI_10017647 (Achaete-scute-like protein 1)
Cgi-Mir-92-o31 CGI_10001538 (Tribbles-like protein 2), CGI_10009355 (Cell division cycle 2-related protein kinase 7), CGI_10009355, CGI_10014759 (Guanine nucleotide-binding protein G(o) subunit alpha), CGI_10017574 (Protein still life, isoforms C)
Cgi-Mir-92-o34 CGI_10001538, CGI_10014759, CGI_10017574, CGI_10026245, CGI_10027167
Cgi-Novel-19 CGI_10001640, CGI_10015879 (Uncharacterized protein C21orf2), CGI_10022346 (Paxillin)
other miRNAs
Cgi-mir-277 CGI_10013946 (Serine), CGI_10014307 (Serine/threonine-protein kinase CTR1), CGI_10020584
Cgi-novel-10 CGI_10013878 (ADP-dependent glucokinase), CGI_10020119 (MAP kinase kinase win1), CGI_10020428 (Latrophilin-3), CGI_10020556 (RAD50-interacting protein 1), CGI_10021961, CGI_10026543 (Membrane progestin receptor gamma-B), CGI_10026562 (Homeobox protein LOX2)
Cgi-mir-750 CGI_10014483 (Contactin), CGI_10016707, CGI_10017867
Cgi-mir-1175 CGI_10001636 (Cytochrome P450 2D28), CGI_10014558 (Heat shock 70 kDa protein 12A), CGI_10014838 (Thrombospondin type-1 domain-containing protein 4), CGI_10017449 (Transcription factor HES-1-B), CGI_10027096 (Activin receptor type-1)