Table 1. Truncated domains in the fusion proteins.

fusion protein	fplen	bp	Pfid	Dlen	Dbeg	Dend	N/C	Dfract	IUleft	IUright	Pfam Desc	Mode of Survival?
MLL-ELL	1966	1406	PF10390	237	4	237	C	0.99	80.1	43.5	RNA pol II ef	no PDB
Col1A1-PDGFB	488	269	PF04692	76	2	76	C	0.99	97.3	64.3	Platelet gf	almost full domain
CBFB-MYH11	553	165	PF02312	171	1	165	N	0.96	38.2	61.4	Core bind f α	almost full domain
RUNX1-CBFA2T3	806	204	PF00853	135	1	130	N	0.96	41.9	67.4	Runt domain	almost full domain
NSD1-ANKRD28	811	412	PF00023	33	3	33	C	0.94	38.6	24.0	Ankyrin	short repeats
TPM4-ALK	784	221	PF00261	237	1	210	N	0.89	52.1	24.4	Tropomyosin	coiled-coil
DAZAP1-MEF2D	390	154	PF00076	70	1	60	N	0.86	50.0	63.5	RNA rec motif	2dgs_A termini IUP (11, 14 aa)
IL2-TNFRSF17	298	117	PF00715	144	1	123	N	0.85	14.8	12.5	Interleukin 2	artefact
MN1-ETV6	1653	1256	PF02198	87	14	87	C	0.85	50.7	30.9	SAM domain	1×66_A N-terminal 18 aa IUP
TMPRSS2-ETV1	422	5	PF04621	333	61	333	C	0.82	62.3	55.1	PEA3 ETS tf N	no PDB
DDX10-NUP98	1462	219	PF00270	171	1	133	N	0.78	22.7	61.7	DEAD b h-ase	1vec_A 151
CDK6-MLL	2599	123	PF00628	53	13	53	C	0.77	29.0	12.5	PHD-finger	1weu_A 12, 17
E2A-PRL	825	483	PF03792	200	56	200	C	0.73	65.7	48.4	PBC domain	no PDB
CLTC-TFE3	1212	932	PF00637	140	1	101	N	0.72	19.7	42.3	Clathrin rep	elongated coil of a-helices
MLL-AFF1	2308	1444	PF05110	1201	338	1201	C	0.72	67.2	72.1	AF-4 oncoprot	no PDB
RUNX1-AFF3	1184	322	PF05110	1205	341	1205	C	0.72	54.3	62.9	AF-4 oncoprot	no PDB
MYH9-ALK	2207	1644	PF01576	858	1	605	N	0.71	55.6	41.4	Myosin tail	no PDB
RABEP1-PDGFRB	1317	738	PF09311	196	1	127	N	0.65	24.8	15.4	Rab5 binding	coiled-coil
NPM-RAR	563	133	PF03066	199	1	121	N	0.61	39.6	21.2	Nucleoplasmin	nucleophosmin 2p1b_H, 122 aa
COL6A3-CSF1	2089	1738	PF00092	174	1	100	N	0.57	40.7	77.8	VWA	1dzi_A 104,114
Col1A1-PDGFB	488	269	PF01391	60	1	34	N	0.57	97.3	64.3	Collagen	coiled-coil, repeat
ETV6-JAK2	622	154	PF07714	261	118	261	C	0.55	31.8	28.0	Tyr kinase	2f4j_A 157, 167
MLL-FOXO3	1910	1444	PF00250	98	50	98	C	0.51	49.1	58.0	Fork head	1jxs_A 43, 53, 63
MSN-ALK	1005	448	PF00769	240	1	111	N	0.46	62.3	34.9	Ezrin	1e5w_A 106, 206, 286, 306
CBFB-MYH11	553	165	PF01576	858	512	858	C	0.40	38.2	61.4	Myosin tail	no PDB
CDK6-MLL	2599	123	PF00069	288	1	114	N	0.40	29.0	12.5	Protein kinase	1g3n_A 89, 94, 104
COL6A3-CSF1	1571	1211	PF05337	268	181	268	C	0.33	32.6	81.2	Mphag CSF1	no PDB
ATIC-ALK	792	229	PF01808	328	1	96	N	0.29	38.2	36.7	AIC/IMPCHase	1p4r_A 200(scop)
RPN1-EVI1	1156	87	PF04597	429	1	59	N	0.14	26.8	31.6	Ribophorin I	no PDB
MLL-CALM	1803	1406	PF07651	267	237	267	C	0.12	71.6	58.8	ANTH domain	1hf8_A 99, 139, 219

Nontrivial cases of fusion proteins are shown where breakpoint falls into a Pfam domain. The abbreviated column identifiers are as follows: Pfid, Pfam identifier; fplen, fusion protein length; bp, breakpoint; Dlen, domain length, Dbeg, Dend, domain match beginning and end, respectively; N/C, the retained half of the truncated domain; Dfract, the retained fraction of the truncated domain; IUleft, IUright, the predicted disorder for the truncated domain and its “mirror” (same number of amino acids as in the truncated domain) on the opposite side of the breakpoint. In the IUleft/IUright columns the value for the truncated domain is italicized whereas the disorder value for its “mirror” is shown in bold. In the last column possible strategies are shown for the truncated domains to follow to avoid elimination by the proteasomal degradation system [49]. “No PDB” indicates the lack of any PDB structures associated with the protein family in question, which together with high predicted disorder values raises the suspicion of the domain being intrinsically disordered. When a PDB code is shown with a list of numbers (shown in bold italic) they indicate positions in the actual domains that are presumably indifferent to truncation based on the exposed hydrophobic surface of the truncated domain (as shown in detail in Figure 4).