DBASS

DBASS3 - Record Details

Gene ATM (Ensembl) Location of 3' Abberant Splice Site
Exon
Phenotype Ataxia telangiectasia (Omim) Distance between Authentic and Aberrant 3' Splice Site (nt)
+7
Mutation IVS11-2A>G Change in the Reading Frame
+1
Splice Site Strength[a]
Authentic Site
Aberrant Site
  Shapiro & Senapathy Matrix
94.41
87.96
Maximum Entropy Model
12.11
1.91
First Order Markov Model
14.26
3.19
Weight Matrix Model
17.84
11.03
Reference(s)

Eng et al. (2004) Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths. Hum. Mutat., 23, 67-76. Pub Med Article # 14695534

Comments
Nucleotide Sequence[b]
tctatatatt tccttttagt ttgttaatgt gatggaatag ttttcaaatt atcctttttt tttttttttt (a>g)gGCTA CAG/ATTGCA ACCCAATTAA TATCAAAGTA TCCTGCAAGT TTACCTAACT GTGAGCTGTC TCCATTACTG ATGATACTAT CTCAGCTTCT ACCCCAACAG CGACATGGGG AACGTACACC ATATGTGTTA CGATGCCTTA CGGAAGTTGC ATTGTGTCAA GACAAGAGGT CAAACCTAGA AAGCTCACAA AAGTCAGATT TATTAAAACT CTGGAATAAA ATTTGGTGTA TTACCTTTCG TGGTATAAGT TCTGAGCAAA TACAAGCTGA AAACTTTGGC TTACTTGGAG CCATAATTCA GGGTAGTTTA GTTGAGGTTG ACAGAGAATT CTGGAAGTTA TTTACTGGGT CAGCCTGCAG ACCTTCATGg
Terminal Exon? No

Legend

[a] Shapiro and Senapathy matrix scores were calculated according to an algorithm published previously (1, 2). Maximum entropy and the first-order Markov and weight matrix models were computed as described (3). Information contents of each splice site was described previously (4,5). [b] /, cryptic or de novo splice sites; > nucleotide substitutions; (), deletions; [], duplications or insertions. Intronic sequences are in lower case (in blue), exons are in upper case.

References

  1. Shapiro, M.B. and Senapathy, P. (1987) RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res., 15, 7155-7174.
  2. Senapathy, P., Shapiro, M.B. and Harris, N.L. (1990) Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project. Methods Enzymol., 183, 252-278.
  3. Yeo, G. and Burge, C.B. (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol., 11, 377-394.
  4. Rogan, P.K., Faux, B.M. and Schneider, T.D. (1998) Information analysis of human splice site mutations. Hum. Mutat., 12, 153-171.
  5. Nalla, V.K. and Rogan, P.K. (2005) Automated splicing mutation analysis by information theory. Hum. Mutat., 25, 334-342.