An integrated system to identify conserved sequence elements
      associated to mRNA splicing



[   GIBBS   ][   5'-flanking Region (Intronic)   ][   Motif #1   ]

Motif Logos

Motif Energy Dot Plot (25 + 12 + 25)

Motif Secondary Structure ( 25 + 12 + 25)

Motif Statistics  
Gene ID Chromosome Strand Exon
1
Intron
1
Exon
2
Intron
2
Exon
3
Intron
3
Exon
4
Intron
4
Exon
5
Intron
5
Exon
6
Intron
6
Exon
7
Intron
7
Exon
8
Intron
8
Exon
9
Intron
9
Exon
10
Intron
10
Exon
11
Intron
11
Exon
12
Intron
12
Exon
13
Intron
13
Exon
14
Intron
14
Exon
15
Intron
15
Exon
16
Intron
16
Exon
17
Intron
17
Exon
18
Intron
18
Exon
19
Intron
19
Exon
20
Intron
20
Exon
21
Intron
21
Exon
22
Intron
22
Exon
23
Intron
23
Exon
24
Intron
24
Exon
25
Intron
25
Exon
26
 
ENSG00000012048 HMM 17 -1                                                                                                                                                          0/0
Use HMM Models to Scan This Gene Set M-->Motif s-->selected region  

Motif Information
Detail ID Gene ID Chromosome Start Position End Position Strand View ProSplicer Splice View
1 ENSG00000012048  17  41649875 41649886 -1
2 ENSG00000012048  17  41649918 41649929 -1
3 ENSG00000012048  17  41650087 41650098 -1
4 ENSG00000012048  17  41650136 41650147 -1
5 ENSG00000012048  17  41650193 41650204 -1
6 ENSG00000012048  17  41650242 41650253 -1
7 ENSG00000012048  17  41649918 41649929 -1
8 ENSG00000012048  17  41650087 41650098 -1
9 ENSG00000012048  17  41650136 41650147 -1
10 ENSG00000012048  17  41650174 41650185 -1
11 ENSG00000012048  17  41650200 41650211 -1
12 ENSG00000012048  17  41650242 41650253 -1
13 ENSG00000012048  17  41629011 41629022 -1
14 ENSG00000012048  17  41624797 41624808 -1
15 ENSG00000012048  17  41624846 41624857 -1
16 ENSG00000012048  17  41624865 41624876 -1
17 ENSG00000012048  17  41624914 41624925 -1
18 ENSG00000012048  17  41620818 41620829 -1
19 ENSG00000012048  17  41620868 41620879 -1
20 ENSG00000012048  17  41620984 41620995 -1
21 ENSG00000012048  17  41621013 41621024 -1

Motif Simplified PSSM
A 0 9 0 0 0 0 0 0 0 4
C 4 0 2 5 9 0 0 0 4 0
G 3 0 7 4 0 3 9 7 5 0
T 0 0 0 0 0 6 0 0 0 3

Motif PSSM
Position A C G T
1 0 41 28 0
3 93 0 0 0
4 0 23 72 0
5 0 54 37 0
6 0 88 0 0
7 0 0 28 55
8 0 0 89 0
9 0 0 72 0
11 0 36 54 0
12 41 0 0 33

Motif FASTA
1 ggtattctt TGACGGGGGGTA ggggcggaac
2 aaggcgttgt GAACCCTGGGGA ggggggcagt
3 gagttccaga CCAGCCTGACCA acgtggtgaa
4 aatacaaaaa TTAGCCGGGCGT ggtgccgctc
5 agaatcgcta GAACCCGGGAGG cggaggttgc
6 ccattgcact CCAGCCTGGGCG acagagcgag
7 aaggcgttgt GAACCCTGGGGA ggggggcagt
8 gagttccaga CCAGCCTGACCA acgtggtgaa
9 aatacaaaaa TTAGCCGGGCGT ggtgccgctc
10 ctcaggaggc TGAGGCAGGAGA atcgctagaa
11 ctagaacccg GGAGGCGGAGGT tgcagtgagc
12 ccattgcact CCAGCCTGGGCG acagagcgag
13 atcatgttgg CCAGGCTGGTCT cgaactccta
14 aaataaaaaa TTAGCCAGGTGT ggtggcacat
15 ctcgggaggc TGAGGCAGGAGA atcacttgaa
16 agaatcactt GAACCCGGGAGG tggaggttgc
17 ccattgcact CCAGCCTGGGCA aaaatagcga
18 actctgttgc CCAGGCTGGAGT gcagtgatgc
19 cctccacctc CAAGGCTCAAGC tatcctccca
20 accatgttac CGAGGCTGGTCT caaactcctg
21 ctggactcaa GCAGTCTGCCCA cttca


Department of Computer Science and Information Engineering
National Central University
No.300, Jung-Da Rd., Chung-li , Tao-yuan, Taiwan, 320, R.O.C.
Department of Biological Science and Technology, Institute of Bioinformatics
National Chiao Tung University
1001 Ta Hsueh Road, Hsinchu, Taiwan 300, ROC
Contact with bryan@mail.NCTU.edu.tw







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