DBASS5 - Record Details
| Gene |
HLA-A*110X (Ensembl) |
Location of Aberrant 5' Splice Site | Intron |
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| Phenotype |
Aberrant HLA class I molecule (OMIM) |
Distance between Authentic and Aberrant 5' Splice Site (nt) |
+18
|
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| Mutation | IVS5+17G>A | Change in the Reading Frame |
0
|
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| Reference(s) |
Tijssen, H.J., Sistermans, E.A. and Joosten, I. (2000) A unique second donor splice site in the intron 5 sequence of the HLA-A*11 alleles results in a class I transcript encoding a molecule with an elongated cytoplasmic domain. Tissue Antigens, 55, 422-428. Pub Med Article # 10885562 |
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| Nucleotide Sequence[a] | AGCTGTCTTC CCAGCCCACC ATCCCCATCG TGGGCATCAT TGCTGGCCTG GTTCTCCTTG GAGCTGTGAT CACTGGAGCT GTGGTCGCTG CCGTGATGTG GAGGAGGAAG AGCTCAGgtg gagaaggggt gaa(g>a)g/ gtggggtctg agatttcttg tctcactgag ggttccaagc cccagctaga aatgtgccct gtctcattac tgggaagcac cttccacaat catgggccga cccagcctgg gccctgtgtg ccagcactta ctcttttgta aagcacctgt taaaatgaag gacagattta tcaccttgat tacggcggtg atgggacctg ataccagcag tcacaagtca caggggaagg tccctgagga cagacctcag gagggctatt ggtccaggac ccacacctgc tttcttcatg tttcctgatc | ||||
| Percent Utilisation | 60 | ||||
| Terminal Exon? | No | ||||
| Splice Site Strength[b] | Authentic Site |
Aberrant Site |
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| Maximum Entropy Model [1] |
2.57
|
2.21
|
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| Maximum Dependence Decomposition Model [2] |
8.88
|
7.48
|
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| First Order Markov Model [1] |
4.44
|
4.10
|
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| Weight Matrix Model [1] |
5.74
|
5.74
|
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| Genomic Co-ordinates (hg38) | |||||
| Aberrant Splice Site |
chr6:29944634/29944635 |
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| Mutation |
chr6:29944633 |
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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). Maximum entropy and the first-order Markov and weight matrix models were computed as described (2)
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.
- Yeo, G. and Burge, C.B. (2004) Maximum entropy modelling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol., 11, 377-394.
- Burge, C. 1998. Modeling dependencies in pre-mRNA splicing signals. In Computational methods in molecular biology (eds. S.L. Salzberg et al.), chapter 8, pp. 129–164. Elsevier Science, Philadelphia, PA.