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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTCAAGGATGGCCTGTGGGATGTCTATAACGATTTCCCGATGGGAATGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgctacttctgctttatttatgaatttcaacatgttatattctacttgcaacaagtttgggcaatgacttattctttcttctag

Basic information

species Zea mays
transcript GRMZM5G860137_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G860137_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g02020.1 (Oryza sativa), 5'ss of exon 4
GATGCTCAAGGATGGCCTGTGGGATGTCTATAACGATTTCCCGATGGGAATGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgctacttctgctttatttatgaatttcaacatgttatattctacttgcaacaagtttgggcaatgacttattctttcttctag
||||||||||||||| ||||||||||| ||||| |||||||| |||||||||||||| || |||||| | || || ||||| || |||||||||||||||||||    |  | ||||   || |  |  |    |  ||||    ||||   || | |  || |   || ||     ||||||||||||
GATGCTCAAGGATGGGCTGTGGGATGTGTATAATGATTTCCCAATGGGAATGTGTGCCGAGTTGTGTGCGGATCAACACTCCATTTCAAGGGAGGAGCAGgttgtcaatgttcctgc---atctgcgcttgcatatttgtttatatctaggagcta-acattggactaaagaacacctctttcttctag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|78180536|gb|DV551029.1|DV551029
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCGGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|149110543|gb|EE190473.2|EE190473
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|89760643|gb|DY688974.1|DY688974
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|149071725|gb|EE160115.2|EE160115
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|93281948|gb|EB674212.1|EB674212
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCCATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGC
EST: gi|149029957|gb|EE286286.2|EE286286
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|149087112|gb|EE176651.2|EE176651
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|74232957|gb|DT640871.1|DT640871
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTA
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTA
EST: gi|6994169|gb|AW453383.1|AW453383
EST:     CCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCGGGATAGC
genomic: CCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|71426143|gb|DR807193.1|DR807193
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|78087866|gb|DV516259.1|DV516259
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCANGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|78078473|gb|DV506886.1|DV506886
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCANGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|148939632|gb|EC884275.2|EC884275
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAAGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|12047245|gb|BF729384.1|BF729384
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCGGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
EST: gi|149084568|gb|EE174037.2|EE174037
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATC
EST: gi|71439486|gb|DR820536.1|DR820536
EST:     TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAG                         GATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC
genomic: TGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

GATGCTCAAGGATGGCCTGTGGGATGTCTATAACGATTTCCCGATGGGAATGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 454

GATGCTCAAGGATGGCCTGTGGGATGTCTATAACGATTTCCCGATGGGAATGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

GATGCTCAAGGATGGCCTGTGGGATGTCTATAACGATTTCCCGATGGGAATGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

GATGCTCAAGGATGGCCTGTGGGATGTCTATAACGATTTCCCGATGGGAATGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgcta ... tttcttctagGATTCGTATGCTATCCTCAGCAATGAACGTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTCAAGGATGGCCTGTGGGATGTCTATAACGATTTCCCGATGGGAATGTGTGCTGAATTGTGTTCAGACCAGCACTCAATCTCAAGGGAGGAGCAGgttgctgctacttctgctttatttatgaatttcaacatgttatattctacttgcaacaagtttgggcaatgacttattctttcttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG