Table III.
Predicted conserved (minimum of two species) PTBP1 binding sites in the mRNA UTRs from regulated proteins
Hits are sorted by p value, p < 0.01. Some genes are listed several times in the table because of a different number of mismatches detected in the PTBP1 consensus sequence and consequently different p values. NECAP, adaptin ear-binding clathrin-associated protein.
| Entrez Gene symbol | Protein | Untranslated region | Number of mismatchesa | Number of hits | p valueb | Number of hits in single strandc |
|---|---|---|---|---|---|---|
| Stau2 | Staufen2 | 3′ | 1 | 9 | 0 | 4 |
| Lmna | Lamin A | 3′ | 2 | 33 | 0 | 12 |
| Dpysl2 | Dihydropyrimidinase-related protein 2 | 3′ | 2 | 42 | 0 | 10 |
| C11orf59 | Chromosome 11 open reading frame 59 | 3′ | 2 | 23 | 0 | 0 |
| Aldoa | Aldolase A | 3′ | 2 | 12 | 0.0001 | 4 |
| Tubb2b | Tubulin β chain 15 | 3′ | 2 | 13 | 0.0001 | 3 |
| Stau2 | Staufen2 | 3′ | 2 | 21 | 0.0001 | 5 |
| Stxbp1 | Syntaxin-binding protein 1 | 3′ | 2 | 36 | 0.0001 | 21 |
| Pkm2 | M2 pyruvate kinase | 3′ | 2 | 18 | 0.0002 | 6 |
| Stau2 | Staufen2 | 3′ | 0 | 2 | 0.0005 | 1 |
| Sgta | Small glutamine-rich tetratricopeptide repeat (TPR)-containing, α | 3′ | 1 | 9 | 0.0006 | 4 |
| Serbp1 | Plasminogen activator inhibitor 1 RNA-binding protein | 5′ | 1 | 3 | 0.0007 | 3 |
| Snx3 | Sorting nexin 3 | 3′ | 1 | 5 | 0.0007 | 2 |
| Glul | Glutamate-ammonia ligase (glutamine synthase) | 3′ | 2 | 19 | 0.0014 | 4 |
| Dpysl2 | Dihydropyrimidinase-related protein 2 | 5′ | 2 | 9 | 0.0018 | 1 |
| Inexa | α-Internexin | 3′ | 2 | 21 | 0.0026 | 6 |
| Stmn1 | Stathmin 1 | 3′ | 1 | 3 | 0.003 | 1 |
| Ndrg1 | N-myc downstream regulated 1 | 3′ | 2 | 17 | 0.003 | 3 |
| Necap1 | NECAP endocytosis-associated 1 | 3′ | 1 | 5 | 0.0032 | 1 |
| Tubb2b | Tubulin β chain 15 | 3′ | 1 | 3 | 0.0037 | 0 |
| Smc3 | Structural maintenance of chromosomes protein 3 | 5′ | 2 | 4 | 0.0038 | 0 |
| Atp6v1a | ATPase, H+-transporting, lysosomal V1 subunit A | 3′ | 2 | 25 | 0.0039 | 6 |
| Pkm2 | M2 pyruvate kinase | 3′ | 1 | 4 | 0.0063 | 1 |
| Stmn1 | Stathmin 1 | 3′ | 2 | 8 | 0.0063 | 4 |
| Pcbp2 | Poly(rC)-binding protein 2 | 3′ | 2 | 9 | 0.0064 | 3 |
| Dpysl2 | Dihydropyrimidinase-related protein 2 | 3′ | 1 | 7 | 0.0065 | 2 |
| Ppp1r8 | Predicted: similar to protein phosphatase 1, regulatory (inhibitor) subunit 8 | 3′ | 2 | 11 | 0.0065 | 4 |
| Cugbp1 | CUG triplet repeat, RNA-binding protein 1 | 3′ | 1 | 4 | 0.0068 | 0 |
| Cmpk | Cytidylate kinase | 3′ | 2 | 11 | 0.0094 | 5 |
| Ppp1cb | Protein phosphatase 1, catalytic subunit, β isoform | 3′ | 2 | 16 | 0.0095 | 1 |
| Ndrg1 | N-myc downstream regulated 1 | 3′ | 1 | 4 | 0.0098 | 1 |
a
Number of mismatches between 0 and 2.
b
The p value is the probability of obtaining at least the same number of hits in a random sequence of the same composition.
c
The secondary structure of RNA was predicted using RNAfold (53).