Table 1.
List of CLIP-Seq-Positive CoTC Candidate Genes
| Gene Symbol | Transcript_ID | Gene Name |
|---|---|---|
| AGFG1 | NM_004504 | ArfGAP with FG repeats 1 |
| AKIRIN1 | NM_001136275 | akirin 1 |
| BCAP29 | NM_001008405 | B cell receptor-associated protein 29 |
| BLCAP | NM_006698 | bladder cancer-associated protein |
| BRD9 | NM_001009877 | bromodomain containing 9 |
| C5orf28 | NM_022483 | chromosome 5 open reading frame 28 |
| C5orf35 | NM_153706 | chromosome 5 open reading frame 35 |
| CANX | NM_001746 | Calnexin |
| CCDC72 | NM_015933 | coiled-coil domain containing 72 |
| CCNB1 | NM_031966 | cyclin B1 |
| CD55 | NM_001114752 | CD55 molecule, decay accelerating factor for complement (Cromer blood group) |
| CELF1 | NM_001172640 | CUGBP Elav-like family member 1 |
| CHST15 | NM_015892 | carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15 |
| CYBRD1 | NM_024843 | cytochrome b reductase 1 |
| CYFIP1 | NM_014608 | cytoplasmic FMR1 interacting protein 1 |
| DDX3X | NM_001356 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked |
| DDX58 | NM_014314 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 |
| DMD | NM_004019 | Dystrophin |
| DNAJC6 | NM_014787 | DnaJ (Hsp40) homolog, subfamily C, member 6 |
| FAM200B | NM_001145191 | family with sequence similarity 200, member B |
| FAR1 | NM_032228 | fatty acyl CoA reductase 1 |
| GNAI3 | NM_006496 | guanine nucleotide binding protein (G protein), α inhibiting activity polypeptide 3 |
| GNB2L1 | NM_006098 | guanine nucleotide binding protein (G protein), β polypeptide 2-like 1 |
| HADHA | NM_000182 | hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), α subunit |
| HBB | NM_000518 | hemoglobin, β |
| HES7 | NM_001165967 | hairy and enhancer of split 7 (Drosophila) |
| HN1L | NM_144570 | hematological and neurological expressed 1-like |
| HNRNPD | NM_031369 | heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37 kDa) |
| HNRNPM | NM_031203 | heterogeneous nuclear ribonucleoprotein M |
| IRX3 | NM_024336 | iroquois homeobox 3 |
| KCMF1 | NM_020122 | potassium channel modulatory factor 1 |
| KLF6 | NM_001160125 | Kruppel-like factor 6 |
| MAFK | NM_002360 | v-maf musculoaponeurotic fibrosarcoma oncogene homolog K (avian) |
| MARK3 | NM_001128920 | MAP/microtubule affinity-regulating kinase 3 |
| MIB1 | NM_020774 | mindbomb homolog 1 (Drosophila) |
| MRPL30 | NM_145212 | mitochondrial ribosomal protein L30 |
| MRPS14 | NM_022100 | mitochondrial ribosomal protein S14 |
| MYC | NM_002467 | v-myc myelocytomatosis viral oncogene homolog (avian) |
| NCS1 | NM_001128826 | frequenin homolog (Drosophila) |
| NQO2 | NM_000904 | NAD(P)H dehydrogenase, quinone 2 |
| NUCKS1 | NM_022731 | nuclear casein kinase and cyclin-dependent kinase substrate 1 |
| NUFIP2 | NM_020772 | nuclear fragile X mental retardation protein interacting protein 2 |
| OMA1 | NM_145243 | OMA1 homolog, zinc metallopeptidase (Saccharomyces cerevisiae) |
| PRPF4B | NM_003913 | similar to hCG1820375; PRP4 pre-mRNA processing factor 4 homolog B (yeast) |
| PSIP1 | NM_021144 | PC4 and SFRS1 interacting protein 1 |
| PTCH2 | NM_001166292 | patched homolog 2 (Drosophila) |
| RAB13 | NM_002870 | RAB13, member RAS oncogene family; similar to hCG24991 |
| RAPH1 | NM_213589 | Ras association (RalGDS/AF-6) and Pleckstrin homology domains 1 |
| RBM27 | NM_018989 | RNA binding motif protein 27 |
| RNASEH1 | NM_002936 | ribonuclease H1 |
| RNF166 | NM_178841 | ring finger protein 166 |
| RPL13A | NM_012423 | ribosomal protein L13a pseudogene |
| RPL37A | NM_000998 | ribosomal protein L37a |
| RRP15 | NM_016052 | ribosomal RNA processing 15 homolog (S. cerevisiae) |
| SAC3D1 | NM_013299 | SAC3 domain containing 1 |
| SAP18 | NM_005870 | Sin3A-associated protein, 18 kDa |
| SCAF8 | NM_014892 | RNA binding motif protein 16 |
| SCLT1 | NM_144643 | sodium channel and clathrin linker 1 |
| SIK1 | NM_173354 | salt-inducible kinase 1 |
| TEAD1 | NM_021961 | TEA domain family member 1 (SV40 transcriptional enhancer factor) |
| TFAP2A | NM_001042425 | transcription factor AP-2 α (activating enhancer binding protein 2 α) |
| THOC2 | NM_001081550 | THO complex 2 |
| TNRC6A | NM_014494 | trinucleotide repeat containing 6A |
| TROAP | NM_001100620 | trophinin-associated protein (tastin) |
| TUBA1B | NM_006082 | hypothetical gene supported by AF081484; NM_006082; tubulin,α 1b |
| TXLNG | NM_001168683 | γ-taxilin |
| TXNRD1 | NM_001093771 | thioredoxin reductase 1; hypothetical LOC100130902 |
| WDR13 | NM_001166426 | WD repeat domain 13 |
| WDR36 | NM_139281 | WD repeat domain 36 |
| WNK1 | NM_014823 | WNK lysine deficient protein kinase 1 |
| YWHAZ | NM_145690 | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, ζ polypeptide |
| ZAK | NM_133646 | sterile α motif and leucine zipper containing kinase AZK |
| ZBTB9 | NM_152735 | zinc finger and BTB domain containing 9 |
| ZDHHC7 | NM_001145548 | zinc finger, DHHC-type containing 7 |
| ZNF215 | NM_013250 | zinc finger protein 215 |
| ZNF616 | NM_178523 | zinc finger protein 616 |
| ZNF714 | NM_182515 | zinc finger protein 714 |
| ZNF740 | NM_001004304 | zinc finger protein 740 |
List of nonredundant RefSeq protein-coding genes containing CstF-64 CLIP regions (supported by at least two read-alignments) within poly(A) site regions (extended 200 nt downstream). These genes represent candidates for the CoTC termination mechanism. “Ribonucleoprotein complex” and “RNA binding” GO-TERMs were significantly enriched (Benjamini < 0.05) among these genes (DAVID Bioinformatics Resources). HBB derives from CLIP1 where cells were transfected with the β-globin expression plasmid βTERM.