CAFTAN: a tool for fast mapping, and quality assessment of cDNAs

del Val, Coral; Kuryshev, Vladimir Yurjevich; Glatting, Karl-Heinz; Ernst, Peter; Hotz-Wagenblatt, Agnes; Poustka, Annemarie; Suhai, Sandor; Wiemann, Stefan

doi:10.1186/1471-2105-7-473

BMC Bioinformatics

Table 5 Selection of cDNAs classified as "bad_single_exon_cdna" by CAFTAN.

From: CAFTAN: a tool for fast mapping, and quality assessment of cDNAs

	VEGA Transcript ID	Description	Transcript name	Problem
1	OTTHUMT00000033440	histone 2, H2ab	HIST2H2AB-001	Histone mRNAs are not polyadenylated.
2	OTTHUMT00000040062	Small proline-rich protein 1A	SPRR1A-001	Fails tail of the 3' end of the cDNA
3	OTTHUMT00000040078	histone 1, H3c	HIST1H3C-001	Histone mRNAs are not polyadenylated.
4	OTTHUMT00000040083	histone 1, H2bb	HIST1H2BB-001	Histone mRNAs are not polyadenylated.
5	OTTHUMT00000040098	histone 1, H3f	HIST1H3F-001	Histone mRNAs are not polyadenylated.
6	OTTHUMT00000040100	histone 1, H2ad	HIST1H2AD-001	Histone mRNAs are not polyadenylated.
7	OTTHUMT00000040108	histone 1, H2bf	HIST1H2BF-001	Histone mRNAs are not polyadenylated.
8	OTTHUMT00000040109	histone 1, H2bg	HIST1H2BG-001	Histone mRNAs are not polyadenylated.
9	OTTHUMT00000040110	histone 1, H2bh	HIST1H2BH-001	Histone mRNAs are not polyadenylated.
10	OTTHUMT00000040111	histone 1, H2bi	HIST1H2BI-001	Histone mRNAs are not polyadenylated.
11	OTTHUMT00000040119	histone 1, H4h	HIST1H4H-001	Histone mRNAs are not polyadenylated.
12	OTTHUMT00000040138	histone 1, H2	HIST1H2BJ-001	Histone mRNAs are not polyadenylated.
13	OTTHUMT00000040154	histone 1, H2aj	HIST1H2AJ-001	Histone mRNAs are not polyadenylated.
14	OTTHUMT00000040160	histone 1, H2al	HIST1H2AL-001	Histone mRNAs are not polyadenylated.
15	OTTHUMT00000040162	histone 1, H2am	HIST1H2AM-001	Histone mRNAs are not polyadenylated.
16	OTTHUMT00000042255		RP11-295F4.3-001	Fails tail of the 3' end of the cDNA
17	OTTHUMT00000042262		TAAR8-001	Signal 70 pb upstream. EST evidence from a shorter gene
18	OTTHUMT00000043372	histone 1, H1c	HIST1H1C-001	Histone mRNAs are not polyadenylated.
19	OTTHUMT00000043452	histone 1, H3i	HIST1H3I-001	Histone mRNAs are not polyadenylated.
20	OTTHUMT00000043453	histone 1, H3j	HIST1H3J-001	Histone mRNAs are not polyadenylated.
21	OTTHUMT00000043884	histone H1	HIST1H1A-002	Histone mRNAs are not polyadenylated.
22	OTTHUMT00000044894	cysteinyl leukotriene receptor 2	CYSLTR2-001	Partial 3'UTR Sequence
23	OTTHUMT00000050610	G protein-coupled receptor 10	GPR10-001	Partial 3'UTR Sequence
24	OTTHUMT00000051889	Interferon, alpha 4	IFNA4-001	Internal primed
25	OTTHUMT00000051905	Interferon, alpha 6	IFNA6-001	Internal primed
26	OTTHUMT00000053504	T-cell acute lymphocytic leukemia 2	TAL2	Internal primed
27	OTTHUMT00000057327	G protein-coupled receptor 174	GPR174	Partial 3'UTR Sequence
28	OTTHUMT00000057879	Insulin receptor substrate 4	IRS4	Ends in the signal,
29	OTTHUMT00000059081	Potassium voltage-gated channel	KCNA10-001	Partial 3'UTR Sequence
30	OTTHUMT00000059124	Taste receptor, type 2, member 4	TAS2R4	Partial 3'UTR Sequence
31	OTTHUMT00000072293	A disintegrin	ADAM21-001	Artifact, much longer than the real gene
32	OTTHUMT00000076126	MAS1 oncogene-like	MAS1L-001	Partial 3'UTR Sequence
33	OTTHUMT00000087128	histone 2, H2ac	HIST2H2AC-001	Histone mRNAs are not polyadenylated.
34	OTTHUMT00000147346		HsG1428-001	Partial 3'UTR Sequence
35	OTTHUMT00000147982		HsG647-001	Partial 3'UTR Sequence
36	OTTHUMT00000147994		HsG684-001	Presence of a repeat in the 3' UTR
37	OTTHUMT000001480 95		HsG2001-001	Partial 3'UTR Sequence

All of them lack the presence of a polyA signal but have a perfect match to VEGA transcripts, as it should be expected. The manual inspection by an expert curator of these VEGA CDNAs showed that 19 all of them are Histone coding cDNAs which do not go under polyadenylation. The rest either did not have a complete 3'UTR region or was an artifact 3'.

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ISSN: 1471-2105

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