Bioinfomatic prediction of IREs by SIREs in novel IRP1 and IRP2 target mRNAs
| Gene name . | Description . | Reference ID . | IRE sequence . | Position . | Motif . | Mismatch . | Bulge . |
|---|---|---|---|---|---|---|---|
| 1 2010107G12Rik | RIKEN cDNA 2010107G12 gene | NM_001025573 | GTTCCGCTTC.C.C. TTACC.CAGGGC.AGTGGG.GCCTCCCCAC | CDS | 8 | N13-N20:C_A | |
| 2 4930579E17Rik | RIKEN cDNA 4930579E17 gene | NM_178629 | GTGGGCAAAC.T.C.TTGCC.TAGTAT.GGATAGA.GCGACATCCC | 3′UTR | 9 | N21b:A | |
| 3 8430410A17Rik | RIKEN cDNA 8430410A17 gene | NM_173737 | GCCGGCGGCG.G.C.TCCCG.CAGTGG.AGGGAC.CCCGACAAGT | CDS | 1 | N13-N20:G_A | |
| 4 A430093A21Rik | RIKEN cDNA A430093A21 gene | NM_001081436 | CTTGTATAAG.C.C.GCCTG.CAGAGA.CTGGTG.AAACTGTGCA | CDS | 2 | N12-N21:T_T | |
| 5 AI450353 | Expressed sequence AI450353 | AK134743 | TGTGAGAGTA.G.C.TTTTT.GAGTGT.GTAAGC.CTACATTTGA | N/A | 17 | N12-N21:T_T | |
| 6 ANKRD29 | Ankyrin repeat domain 29 | NM_173505 | ATCTTGAGTT.T.C.CAACA.CCGTGC.TGCTTGA.TAGAATGACT | 3′UTR | 4 | N21b:C | |
| 7 BC051227 | cDNA sequence BC051227 | NM_183170 | TGCGCGCGCG.G.C.CTGGA.CAGAGA.TTCAGC.GCGCGGCGCT | CDS | 2 | ||
| 8 Cxcl16 | Chemokine (C-X-C motif) ligand 16 | NM_023158 | AGCAGGCTCG.T.C.TCCAT.CAGTGA.ATGGAA.CCTGAGCTCA | 3′UTR | 1 | ||
| 9 Dlg2 | Discs, large homolog 2 (Drosophila) | NM_011807 | GACTACGAAG.T.C.GACGG.CAGAGA.CTATCA.CTTTGTCATT | CDS | 2 | N11-N22:C_A | |
| DLG2 | Discs, large homolog 2 (Drosophila) | NM_001364 | AAGAGATAGA.G.C.CATCA.GAGTGA.TGGGGC.TTCTTCACAG | 3′UTR | 17 | N10-N23:A_G | |
| 10 Egr2 | Early growth response 2 | NM_010118 | TGGCAGTGGG.T.C.TGCAG.CAGTGA.CTGCCA.CCCCTTATAA | CDS | 1 | N09-N24:T_C | |
| 11 FXYD5 | FXYD domain containing ion transport regulator 5 | NM_144779 | CCTCCTTGCG.T.C.AGTCC.CAGTGA.GGGATA.AGCGCCTGGC | 5′UTR | 1 | N10-N23:G_A | |
| 12 Garnl1 | GTPase activating RANGAP domain-like 1 | NM_019994 | TTTACACTCT.C.C.AGATT.CAGAGC.GGTCTT.CTAAACTGCA | CDS | 2 | N07-N25:C_T | |
| Garnl1 | GTPase activating RANGAP domain-like 1 | NM_001003719 | GTCGTCGGGA.C.C.CGGCC.GGGAGG.GGCCGC.GGCGGCCGCA | 5′UTR | 16 | N07-N25:C_C | |
| 13 Gstm6 | Glutathione S-transferase, mu 6 | NM_008184 | TATGCAGGCT.C.C.ATCTC.CAGAGT.GGGAAG.GCCCAGTCTT | 3′UTR | 2 | N09-N24:A_A | |
| 14 Gstt3 | Glutathione S-transferase, theta 3 | NM_133994 | TGACTTGGTG.G.C.CATCA.CAGAGC.TGATGC.ATCCTGTCAG | CDS | 2 | ||
| 15 Gyg | Glycogenin | NM_013755 | ATCAGCAGCA.C.C.AGACC.CAGGGT.GGCCTG.ACTGTTTCAA | CDS | 8 | N11-N22:A_C | |
| GYG1 | Glycogenin-1 | NM_004130 | GTCAGCAGCA.C.C.AGACC.CAGGGT.GGCCTG.ACTGCTTCAA | CDS | 8 | N11-N22:A_C | |
| GYG1 | Glycogenin-1 | NM_004130 | CAGATGAGAG.G.C.TTTTT.TAGGAT.AAGAGG.TGAGAACTGG | 3′UTR | 10 | N07-N25:G_G | |
| 16 Hao1 | Hydroxyacid oxidase 1, liver | NM_010403 | TCATTTATAG.T.C.ACATT.CAGTGT.AAAGTA.CATATTTTGT | 3′UTR | 1 | N11-N22:A_A | |
| 17 Kcnf1 | Potassium voltage-gated channel, subfamily F, member 1 | NM_201531 | ATTTTGTGAA.T.C.GTGAA.TAGTAC.TTTACA.TTCAAAATTT | 3′UTR | 9 | ||
| Kcnf1 | Potassium voltage-gated channel, subfamily F, member 1 | NM_201531 | CAAAGGCTAA.G.C.TGGGC.CAGTGG.GCCTAA.CCCTTTATGG | 3′UTR | 1 | N07-N25:G_A | |
| 18 Lrpap1 | Low-density lipoprotein receptor-related protein associated protein 1 | NM_013587 | CTTCCCAGAA.C.C.CTCAG.CAGTGT.CTGAGG.CTCAGAGAAA | 3′UTR | 1 | ||
| 19 NR4A3 | Nuclear receptor subfamily 4, group A, member 3 | NM_173199 | CCGCTCACCG.C.C.TCCGG.GAGCCG.CTGGGC.TTGTACACCG | 5′UTR | 14 | N07-N25:C_C | |
| 20 ORMDL1 | ORM1-like 1 (Saccharomyces. cerevisiae) | NM_016467 | TAAGTTAAAG.G.G.CATCA.CAGTGA.GGGTGT.AGTAGATAAA | 3′UTR | 18 | N13-N20:A_G | |
| 21 Pabpc4l | Poly(A) binding protein, cytoplasmic 4-like | NM_001101479 | GTCTTTGGGT.C.C.ATTTG.CAGGGT.TAAAGTG.ATGCAGGAAG | CDS | 8 | N22b:A | |
| 22 Ppp1r1b | Protein phosphatase 1, regulatory subunit 1B | NM_144828 | TTTCCTGGGT.G.C.GGGGA.CAGTGC.TCCTCC.TCCTCCTCCG | 5′UTR | 1 | ||
| 23 PYROXD1 | Pyridine nucleotide-disulfide oxidoreductase domain 1 | NM_024854 | GTCAGTTACA.G.C.TGATA.CAGAGA.TGTGGC.CTGTCTATGT | CDS | 2 | N10-N23:G_G | |
| 24 TP53INP2 | Tumor protein p53 inducible nuclear protein 2 | NM_021202 | TAGGTCAGCG.T.G.CAGAG.CAGTGA.TGCTGG.AGGACACACC | 3′UTR | 18 | N12-N21:A_G |
| Gene name . | Description . | Reference ID . | IRE sequence . | Position . | Motif . | Mismatch . | Bulge . |
|---|---|---|---|---|---|---|---|
| 1 2010107G12Rik | RIKEN cDNA 2010107G12 gene | NM_001025573 | GTTCCGCTTC.C.C. TTACC.CAGGGC.AGTGGG.GCCTCCCCAC | CDS | 8 | N13-N20:C_A | |
| 2 4930579E17Rik | RIKEN cDNA 4930579E17 gene | NM_178629 | GTGGGCAAAC.T.C.TTGCC.TAGTAT.GGATAGA.GCGACATCCC | 3′UTR | 9 | N21b:A | |
| 3 8430410A17Rik | RIKEN cDNA 8430410A17 gene | NM_173737 | GCCGGCGGCG.G.C.TCCCG.CAGTGG.AGGGAC.CCCGACAAGT | CDS | 1 | N13-N20:G_A | |
| 4 A430093A21Rik | RIKEN cDNA A430093A21 gene | NM_001081436 | CTTGTATAAG.C.C.GCCTG.CAGAGA.CTGGTG.AAACTGTGCA | CDS | 2 | N12-N21:T_T | |
| 5 AI450353 | Expressed sequence AI450353 | AK134743 | TGTGAGAGTA.G.C.TTTTT.GAGTGT.GTAAGC.CTACATTTGA | N/A | 17 | N12-N21:T_T | |
| 6 ANKRD29 | Ankyrin repeat domain 29 | NM_173505 | ATCTTGAGTT.T.C.CAACA.CCGTGC.TGCTTGA.TAGAATGACT | 3′UTR | 4 | N21b:C | |
| 7 BC051227 | cDNA sequence BC051227 | NM_183170 | TGCGCGCGCG.G.C.CTGGA.CAGAGA.TTCAGC.GCGCGGCGCT | CDS | 2 | ||
| 8 Cxcl16 | Chemokine (C-X-C motif) ligand 16 | NM_023158 | AGCAGGCTCG.T.C.TCCAT.CAGTGA.ATGGAA.CCTGAGCTCA | 3′UTR | 1 | ||
| 9 Dlg2 | Discs, large homolog 2 (Drosophila) | NM_011807 | GACTACGAAG.T.C.GACGG.CAGAGA.CTATCA.CTTTGTCATT | CDS | 2 | N11-N22:C_A | |
| DLG2 | Discs, large homolog 2 (Drosophila) | NM_001364 | AAGAGATAGA.G.C.CATCA.GAGTGA.TGGGGC.TTCTTCACAG | 3′UTR | 17 | N10-N23:A_G | |
| 10 Egr2 | Early growth response 2 | NM_010118 | TGGCAGTGGG.T.C.TGCAG.CAGTGA.CTGCCA.CCCCTTATAA | CDS | 1 | N09-N24:T_C | |
| 11 FXYD5 | FXYD domain containing ion transport regulator 5 | NM_144779 | CCTCCTTGCG.T.C.AGTCC.CAGTGA.GGGATA.AGCGCCTGGC | 5′UTR | 1 | N10-N23:G_A | |
| 12 Garnl1 | GTPase activating RANGAP domain-like 1 | NM_019994 | TTTACACTCT.C.C.AGATT.CAGAGC.GGTCTT.CTAAACTGCA | CDS | 2 | N07-N25:C_T | |
| Garnl1 | GTPase activating RANGAP domain-like 1 | NM_001003719 | GTCGTCGGGA.C.C.CGGCC.GGGAGG.GGCCGC.GGCGGCCGCA | 5′UTR | 16 | N07-N25:C_C | |
| 13 Gstm6 | Glutathione S-transferase, mu 6 | NM_008184 | TATGCAGGCT.C.C.ATCTC.CAGAGT.GGGAAG.GCCCAGTCTT | 3′UTR | 2 | N09-N24:A_A | |
| 14 Gstt3 | Glutathione S-transferase, theta 3 | NM_133994 | TGACTTGGTG.G.C.CATCA.CAGAGC.TGATGC.ATCCTGTCAG | CDS | 2 | ||
| 15 Gyg | Glycogenin | NM_013755 | ATCAGCAGCA.C.C.AGACC.CAGGGT.GGCCTG.ACTGTTTCAA | CDS | 8 | N11-N22:A_C | |
| GYG1 | Glycogenin-1 | NM_004130 | GTCAGCAGCA.C.C.AGACC.CAGGGT.GGCCTG.ACTGCTTCAA | CDS | 8 | N11-N22:A_C | |
| GYG1 | Glycogenin-1 | NM_004130 | CAGATGAGAG.G.C.TTTTT.TAGGAT.AAGAGG.TGAGAACTGG | 3′UTR | 10 | N07-N25:G_G | |
| 16 Hao1 | Hydroxyacid oxidase 1, liver | NM_010403 | TCATTTATAG.T.C.ACATT.CAGTGT.AAAGTA.CATATTTTGT | 3′UTR | 1 | N11-N22:A_A | |
| 17 Kcnf1 | Potassium voltage-gated channel, subfamily F, member 1 | NM_201531 | ATTTTGTGAA.T.C.GTGAA.TAGTAC.TTTACA.TTCAAAATTT | 3′UTR | 9 | ||
| Kcnf1 | Potassium voltage-gated channel, subfamily F, member 1 | NM_201531 | CAAAGGCTAA.G.C.TGGGC.CAGTGG.GCCTAA.CCCTTTATGG | 3′UTR | 1 | N07-N25:G_A | |
| 18 Lrpap1 | Low-density lipoprotein receptor-related protein associated protein 1 | NM_013587 | CTTCCCAGAA.C.C.CTCAG.CAGTGT.CTGAGG.CTCAGAGAAA | 3′UTR | 1 | ||
| 19 NR4A3 | Nuclear receptor subfamily 4, group A, member 3 | NM_173199 | CCGCTCACCG.C.C.TCCGG.GAGCCG.CTGGGC.TTGTACACCG | 5′UTR | 14 | N07-N25:C_C | |
| 20 ORMDL1 | ORM1-like 1 (Saccharomyces. cerevisiae) | NM_016467 | TAAGTTAAAG.G.G.CATCA.CAGTGA.GGGTGT.AGTAGATAAA | 3′UTR | 18 | N13-N20:A_G | |
| 21 Pabpc4l | Poly(A) binding protein, cytoplasmic 4-like | NM_001101479 | GTCTTTGGGT.C.C.ATTTG.CAGGGT.TAAAGTG.ATGCAGGAAG | CDS | 8 | N22b:A | |
| 22 Ppp1r1b | Protein phosphatase 1, regulatory subunit 1B | NM_144828 | TTTCCTGGGT.G.C.GGGGA.CAGTGC.TCCTCC.TCCTCCTCCG | 5′UTR | 1 | ||
| 23 PYROXD1 | Pyridine nucleotide-disulfide oxidoreductase domain 1 | NM_024854 | GTCAGTTACA.G.C.TGATA.CAGAGA.TGTGGC.CTGTCTATGT | CDS | 2 | N10-N23:G_G | |
| 24 TP53INP2 | Tumor protein p53 inducible nuclear protein 2 | NM_021202 | TAGGTCAGCG.T.G.CAGAG.CAGTGA.TGCTGG.AGGACACACC | 3′UTR | 18 | N12-N21:A_G |
Motif refers to type of apical loop as defined in supplemental Table 3.