DBASS3 - Record Details
| Gene |
RPGR (Ensembl) |
Location of Aberrant 3' Splice Site | Intron |
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| Phenotype |
Retinitis pigmentosa (OMIM 1, OMIM 2, OMIM 3) |
Distance between Authentic and Aberrant 3' Splice Site (nt) |
-7
|
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| Mutation | IVS13-8A>G | Change in the Reading Frame |
+1
|
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| Reference(s) |
Fujita et al. (1997) Analysis of the RPGR gene in 11 pedigrees with the retinitis pigmentosa type 3 genotype: paucity of mutations in the coding region but splice defects in two families. Am. J. Hum. Genet., 61, 571-580. Pub Med Article # 9326322 |
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| Nucleotide Sequence[a] | tgttactaaa tcaaaattag atgtatcaca gactagagag tggcacaaat gatccttaaa gaaaacaaaa ctttagcaaa atatctggta aaacttgcta ttttgattct cctaaactta taaaaatgta aaatcttggc agtatttaaa gtagataagt tgtccttgtc aactaatagt agtatgacat atgataatta cttcaaaaa( a>g)/tttac agAAACAACA AACAATTGGG GAACTGACGC AGGATACAGC TCTTACTGAA AACGATGATA GTGATGAATA TGAAGAAATG TCAGAAATGA AAGAAGGGAA AGCATGTAAA CAACATGTGT CACAAGGGAT TTTCATGACG CAGCCAGCTA CGACTATCGA AGCATTTTCA GATGAGGAAG TAGGTAATGA CACAGGCCAG GTGGGACCTC AGGCTGACAC TGATGGAGAG GGTTTACAAA AAGAGGTATA TAGACATGAA AATAATAATG GTGTTGATCA ACTTGATGCT | ||||
| Terminal Exon? | Yes | ||||
| Splice Site Strength[b] | Authentic Site |
Aberrant Site |
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| Maximum Entropy Model |
5.14
|
0.01
|
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| First Order Markov Model |
4.15
|
0.08
|
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| Weight Matrix Model |
-0.36
|
-2.74
|
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| Genomic Co-ordinates (hg38) | |||||
| Aberrant Splice Site |
chrX:38288048/38288049 |
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| Mutation |
chrX:38288049 |
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Legend
- [a] /, 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 (in green)
- [b] 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).
References
- 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.
- 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.
- 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.