Suppl Table S2. TCF4 Consensus CDS (CCDS)
| Standard transcripts | In-frame splice variants | |||||
| Total exons | Coding exons | Shared exons | CCDS code | Isoform length | CCDS code | Isoform length |
| 20 | 2-19 | 1-19 | CCDS42438.1 | 671 (a) | CCDS11960.1, CCDS82257.1, CCDS58630.1 | 667* (b),670º (o),677 (e) |
| 21 | 1-20 | 2-19 | CCDS58631.1 | 773 (c) | ||
| 19 | 2-18 | 3-19 | CCDS58629.1 | 647 (d) | CCDS77192.1 [NM_001348220.1] | 643* (m), 642*§ (u) |
| 19 | 1-18 | 3-19 | CCDS59321.1 | 664º (f) | ||
| 18 | 1-17 | 4-19 | [NM_001348211.1] | 629 (q) | CCDS58628.1 | 625*§ (g) |
| 16 | 1-15 | 6-19 | CCDS58627.1 | 600§ (h) | CCDS77191.1 | 596*  |
| 15 16 | 2-15 3-15 | 7-19 6-19 | CCDS82255.1 [NM_001348213.1] | 541 (p) 541 (p) | CCDS58626.1 | 537*  |
| 13 | 1-12 | 9-19 | CCDS58624.1 | 511 (j) | CCDS58625.1 [NM_001348214.1] | 507* (k) 506*§ (r) |
| 13 | 1-12 | 9-19 | [NM_001348216.1] | 511 (t) | CCDS58623.1 | 507* (l) |
| 13 | 2-12 | 9-19 | [NM_001348215.1] | 455 (s) |
Notes:
The table lists the different isoforms of the TCF4 protein for which a CCDS entry is available (CCDS) (i.e.: isoforms that are consistently annotated in different databases, including RefSeq, www.ncbi.nlm.nih.gov/refseq/, and Ensembl, www.ensembl.org).
The CCDS entry CCDS42438.1 corresponds to transcript NM_001083962.1, which is usually used in scientific literature as standard reference for TCF4 variant numbering and is used throughout this paper for exon numbering.
The column “Shared exons” indicates the exons of the transcript NM_001083962.1 that are in commons with the other isoforms, not including exon 20 that only encodes for 3’UTR.
RefSeq transcripts coding for protein isoforms not included in the CCDS database are indicated in square brackets.
The letter of the corresponding RefSeq isoform is indicated in round brackets.
The category “In-frame splice variants” includes those isoforms encoded by transcripts that use alternate in-frame splice sites at level of certain exons, compared to the corresponding “Standard transcripts”. Specifically:
- * = -12 bps at the 3’ end of exon 17
- º = -3 bps at the 5’ end of exon 14
- ** = +18 bps at the 5’ end of exon 9'
- § = -3bps at the 5’ end of exon 7
No transcript in the RefSeq and CCDS databases undergoes alternative splicing of internal exons (i.e.: all the downstream internal exons are used considering any alternative 5’ exon). In other databases (e.g.: Ensembl) some transcripts show the skipping of internal exons, with specific focus on exons 7 and 8, which encode for the NLS (Nuclear Localization Sequence).
