Table 3.
Cpeb4 motifs spanning the 17-aa and 8-aa regions predicted with the aid of ELM. The motifs in red are missing in the 8-aa deletion isoform; the ones in dark blue are missing in the 17-aa deletion isoform; motifs in both colors are missing in the isoform with 17-aa and 8-aa deletions.
| Elm name | Instances | Positions | Elm description | Pattern |
|---|---|---|---|---|
| CLV_NDR_NDR_1 | RRG | 34–36 | N-Arg dibasic convertase (nardilysine) cleavage site (Xaa-|-Arg-Lys or Arg-|-Arg-Xaa) | .RK|RR[^KR] |
| CLV_PCSK_PC7_1 | RTYGRRR | 29–35 | Proprotein convertase 7 (PC7, PCSK7) cleavage site (Arg-Xaa-Xaa-Xaa-[Arg/Lys]-Arg-|-Xaa) | [R]...[KR]R. |
| LIG_14-3-3_2 | RGQSSLF | 35–41 | Longer mode 2 interacting phospho-motif for 14-3-3 proteins with key conservation RxxxS#p. | R..[^P][ST] [IVLM]. |
| LIG_BRCT_BRCA1_1 | QSSLF | 37–41 | Phosphopeptide motif which directly interacts with the BRCT (carboxy-terminal) domain of the Breast Cancer Gene BRCA1 with low affinity | .S..F |
| LIG_Clathr_ClatBox_1 | LFPME | 40–44 | Clathrin box motif found on cargo adaptor proteins, it interacts with the beta propeller structure located at the N-terminus of Clathrin heavy chain. | L[IVLMF]. [IVLMF][DE] |
| LIG_PDZ_3 | NDSI | 6–9 | Class III PDZ domains binding motif | .[DE].[IVL] |
| MOD_CK1_1 | SDSSLLI | 20–26 | CK1 phosphorylation site | S..([ST])... |
| MOD_Cter_Amidation | YGRR | 31–34 | Peptide C-terminal amidation | (.)G[RK][RK] |
| MOD_GSK3_1 | LNYSYPGS | 13–20 | GSK3 phosphorylation recognition site | ...([ST])...[ST] |
| MOD_N-GLC_1 | ENDSIK | 5–10 | Generic motif for N-glycosylation. Shakin-Eshleman et al. showed that Trp, Asp, and Glu are uncommon before the Ser/Thr position. Efficient glycosylation usually occurs when ~60 residues or more separate the glycosylation acceptor site from the C-terminus | .(N)[^P][ST].. |
| LNYSYP | 13–18 | |||
| MOD_PKB_1 | RRRGQSSLF | 33–41 | Pkb Phosphorylation site | R.R..([ST])... |
| MOD_PLK | SDSSLLI | 20–26 | Site phosphorylated by the Polo-like-kinase | .[DE].[ST] [ILFWMVA].. |
| TRG_LysEnd_ APsAcLL_1 |
DSSLLI | 21–26 | Sorting and internalisation signal found in the cytoplasmic juxta-membrane region of type I transmembrane proteins. Targets them from the Trans Golgi Network to the lysosomal-endosomal-melanosomal compartments. Interacts with adaptor protein (AP) complexes | [DER]...L[LVI] |
Note: The numeric positions in column 3 are based on the following sequence investigated: IMRAENDSIKGRLNYSYPGSDSSLLINARTYGRRRG QSSLFPMED. The letters in bold represent the 25-aa (the 17-aa plus the 8-aa) region.