Description: SynaMap™ is an application for accurately mapping the exon positions of a selected query sequence using SynaBASE patterns. SynaMap is also designed to recognize splice sites for more accurate mapping of exon positions within a particular genome.
Application Example: A transcript variant of the Homo sapiens amyloid beta (A4) precursor protein (NM_000484.2), which plays a role in Alzheimer’s disease, was used to showcase SynaMap’s specificity by mapping against the Human genome. SynaMap was able to identify the positions of 18 exons on chromosome 21 in 401 milliseconds (Figure 1). In comparison, we have highlighted that BLASTN incorrectly reports 2 separate alignments for exons 1 and 6 (Table 1).
To try SynaMap, please:
  1. Click here and then click on the “Access Now” button.
  2. Click “SynaMap”.
  3. Click on the “Test Sequence” and get the Newsbyte test sequence labelled ‘Homo sapiens amyloid beta (A4) precursor protein’ by clicking on the “Copy” button next to the sequence.
  4. The ‘Homo sapiens genome (NCBI Build 36 v1)’ SynaBASE should be selected.
  5. Using the default parameters given, click on ‘MAP’ to begin your analysis.

Figure 1:  SynaMap results page showing the presence of 18 exons and their positions.

Table 1:  The exon positions as reported by SynaMap and BLASTN where BLASTN reports two separate alignments for exons 1 and 6.

Figure 2:  BLASTN (v2.2.14) relevant alignments - exon 6 alignments.

Figure 3:  BLASTN (v2.2.14) relevant alignments - exon 1 alignments.


Figure 4:  SynaMap screenshot of alignments for exons 1 and 6 showing complete exon coverage (exons flagged by splice site junctions).

Figure 5:  SynaMap results on the UCSC browser where SynaMap exons align well with those published by RefSeq and GenBank.
Test Sequence :

>gi|41406053|ref|NM_000484.2| Homo sapiens amyloid beta (A4) precursor protein (peptidase nexin-II, Alzheimer disease) (APP), transcript variant 1, mRNA
GCTGACTCGCCTGGCTCTGAGCCCCGCCGCCGCGCTCGGGCTCCGTCAGTTTCCTCGGCAGCGGTAGGCG AGAGCACGCGGAGGAGCGTGCGCGGGGGCCCCGGGAGACGGCGGCGGTGGCGGCGCGGGCAGAGCAAGGA CGCGGCGGATCCCACTCGCACAGCAGCGCACTCGGTGCCCCGCGCAGGGTCGCGATGCTGCCCGGTTTGG CACTGCTCCTGCTGGCCGCCTGGACGGCTCGGGCGCTGGAGGTACCCACTGATGGTAATGCTGGCCTGCT GGCTGAACCCCAGATTGCCATGTTCTGTGGCAGACTGAACATGCACATGAATGTCCAGAATGGGAAGTGG GATTCAGATCCATCAGGGACCAAAACCTGCATTGATACCAAGGAAGGCATCCTGCAGTATTGCCAAGAAG TCTACCCTGAACTGCAGATCACCAATGTGGTAGAAGCCAACCAACCAGTGACCATCCAGAACTGGTGCAA GCGGGGCCGCAAGCAGTGCAAGACCCATCCCCACTTTGTGATTCCCTACCGCTGCTTAGTTGGTGAGTTT GTAAGTGATGCCCTTCTCGTTCCTGACAAGTGCAAATTCTTACACCAGGAGAGGATGGATGTTTGCGAAA CTCATCTTCACTGGCACACCGTCGCCAAAGAGACATGCAGTGAGAAGAGTACCAACTTGCATGACTACGG CATGTTGCTGCCCTGCGGAATTGACAAGTTCCGAGGGGTAGAGTTTGTGTGTTGCCCACTGGCTGAAGAA AGTGACAATGTGGATTCTGCTGATGCGGAGGAGGATGACTCGGATGTCTGGTGGGGCGGAGCAGACACAG ACTATGCAGATGGGAGTGAAGACAAAGTAGTAGAAGTAGCAGAGGAGGAAGAAGTGGCTGAGGTGGAAGA AGAAGAAGCCGATGATGACGAGGACGATGAGGATGGTGATGAGGTAGAGGAAGAGGCTGAGGAACCCTAC GAAGAAGCCACAGAGAGAACCACCAGCATTGCCACCACCACCACCACCACCACAGAGTCTGTGGAAGAGG TGGTTCGAGAGGTGTGCTCTGAACAAGCCGAGACGGGGCCGTGCCGAGCAATGATCTCCCGCTGGTACTT TGATGTGACTGAAGGGAAGTGTGCCCCATTCTTTTACGGCGGATGTGGCGGCAACCGGAACAACTTTGAC ACAGAAGAGTACTGCATGGCCGTGTGTGGCAGCGCCATGTCCCAAAGTTTACTCAAGACTACCCAGGAAC CTCTTGCCCGAGATCCTGTTAAACTTCCTACAACAGCAGCCAGTACCCCTGATGCCGTTGACAAGTATCT CGAGACACCTGGGGATGAGAATGAACATGCCCATTTCCAGAAAGCCAAAGAGAGGCTTGAGGCCAAGCAC CGAGAGAGAATGTCCCAGGTCATGAGAGAATGGGAAGAGGCAGAACGTCAAGCAAAGAACTTGCCTAAAG CTGATAAGAAGGCAGTTATCCAGCATTTCCAGGAGAAAGTGGAATCTTTGGAACAGGAAGCAGCCAACGA GAGACAGCAGCTGGTGGAGACACACATGGCCAGAGTGGAAGCCATGCTCAATGACCGCCGCCGCCTGGCC CTGGAGAACTACATCACCGCTCTGCAGGCTGTTCCTCCTCGGCCTCGTCACGTGTTCAATATGCTAAAGA AGTATGTCCGCGCAGAACAGAAGGACAGACAGCACACCCTAAAGCATTTCGAGCATGTGCGCATGGTGGA TCCCAAGAAAGCCGCTCAGATCCGGTCCCAGGTTATGACACACCTCCGTGTGATTTATGAGCGCATGAAT CAGTCTCTCTCCCTGCTCTACAACGTGCCTGCAGTGGCCGAGGAGATTCAGGATGAAGTTGATGAGCTGC TTCAGAAAGAGCAAAACTATTCAGATGACGTCTTGGCCAACATGATTAGTGAACCAAGGATCAGTTACGG AAACGATGCTCTCATGCCATCTTTGACCGAAACGAAAACCACCGTGGAGCTCCTTCCCGTGAATGGAGAG TTCAGCCTGGACGATCTCCAGCCGTGGCATTCTTTTGGGGCTGACTCTGTGCCAGCCAACACAGAAAACG AAGTTGAGCCTGTTGATGCCCGCCCTGCTGCCGACCGAGGACTGACCACTCGACCAGGTTCTGGGTTGAC AAATATCAAGACGGAGGAGATCTCTGAAGTGAAGATGGATGCAGAATTCCGACATGACTCAGGATATGAA GTTCATCATCAAAAATTGGTGTTCTTTGCAGAAGATGTGGGTTCAAACAAAGGTGCAATCATTGGACTCA TGGTGGGCGGTGTTGTCATAGCGACAGTGATCGTCATCACCTTGGTGATGCTGAAGAAGAAACAGTACAC ATCCATTCATCATGGTGTGGTGGAGGTTGACGCCGCTGTCACCCCAGAGGAGCGCCACCTGTCCAAGATG CAGCAGAACGGCTACGAAAATCCAACCTACAAGTTCTTTGAGCAGATGCAGAACTAGACCCCCGCCACAG CAGCCTCTGAAGTTGGACAGCAAAACCATTGCTTCACTACCCATCGGTGTCCATTTATAGAATAATGTGG GAAGAAACAAACCCGTTTTATGATTTACTCATTATCGCCTTTTGACAGCTGTGCTGTAACACAAGTAGAT GCCTGAACTTGAATTAATCCACACATCAGTAATGTATTCTATCTCTCTTTACATTTTGGTCTCTATACTA CATTATTAATGGGTTTTGTGTACTGTAAAGAATTTAGCTGTATCAAACTAGTGCATGAATAGATTCTCTC CTGATTATTTATCACATAGCCCCTTAGCCAGTTGTATATTATTCTTGTGGTTTGTGACCCAATTAAGTCC TACTTTACATATGCTTTAAGAATCGATGGGGGATGCTTCATGTGAACGTGGGAGTTCAGCTGCTTCTCTT GCCTAAGTATTCCTTTCCTGATCACTATGCATTTTAAAGTTAAACATTTTTAAGTATTTCAGATGCTTTA GAGAGATTTTTTTTCCATGACTGCATTTTACTGTACAGATTGCTGCTTCTGCTATATTTGTGATATAGGA ATTAAGAGGATACACACGTTTGTTTCTTCGTGCCTGTTTTATGTGCACACATTAGGCATTGAGACTTCAA GCTTTTCTTTTTTTGTCCACGTATCTTTGGGTCTTTGATAAAGAAAAGAATCCCTGTTCATTGTAAGCAC TTTTACGGGGCGGGTGGGGAGGGGTGCTCTGCTGGTCTTCAATTACCAAGAATTCTCCAAAACAATTTTC TGCAGGATGATTGTACAGAATCATTGCTTATGACATGATCGCTTTCTACACTGTATTACATAAATAAATT AAATAAAATAACCCCGGGCAAGACTTTTCTTTGAAGGATGACTACAGACATTAAATAATCGAAGTAATTT TGGGTGGGGAGAAGAGGCAGATTCAATTTTCTTTAACCAGTCTGAAGTTTCATTTATGATACAAAAGAAG ATGAAAATGGAAGTGGCAATATAAGGGGATGAGGAAGGCATGCCTGGACAAACCCTTCTTTTAAGATGTG TCTTCAATTTGTATAAAATGGTGTTTTCATGTAAATAAATACATTCTTGGAGGAGCAAAAAAAAAAAAAA
A