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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCGGCGAAGGGTTTCGGACAGAGAAGATGGCGACGGCGGCGGCAGGGTTGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtctacctccccatacttcgacacctctatttttgtttcgtgtagttctccacgcaagcttcctgctactgttctccgaattcggctggtggatgagagaaataatttgccgcatggatttggtttggtctgcgcag

Basic information

species Zea mays
transcript GRMZM5G885473_T01
intron # 1
splice site 5'
intron type U2

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|211428534|gb|FL148328.1|FL148328
EST:     TGGCTCCGGCAAAGGAGGTGGTGGASAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|19058471|gb|BM737138.1|BM737138
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211425939|gb|FL148314.1|FL148314
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGASSTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211425945|gb|FL148320.1|FL148320
EST:     GGCTCCGGCAAAGGAGGTGGTGGAGAAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: GGCTCCGGCAAAGGAGGTGGTGGAG-AAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211428542|gb|FL148336.1|FL148336
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|19058470|gb|BM737137.1|BM737137
EST:     TGGCTCCGGCAAAGGAGGTGG-GGAGAAGAAGG-GGAACTCCTGAAGGAG                         ATACGGGCGCACGAGG-GGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|19058567|gb|BM737234.1|BM737234
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211425948|gb|FL148323.1|FL148323
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|67017365|gb|CO446114.1|CO446114
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|87153639|gb|DY398428.1|DY398428
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|22490625|gb|BU050548.1|BU050548
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211204039|gb|FL263373.1|FL263373
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACG
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACG
EST: gi|211428543|gb|FL148337.1|FL148337
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211428541|gb|FL148335.1|FL148335
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211425938|gb|FL148313.1|FL148313
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211428533|gb|FL148327.1|FL148327
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211428532|gb|FL148326.1|FL148326
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211425946|gb|FL148321.1|FL148321
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211428531|gb|FL148325.1|FL148325
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211431128|gb|FL148341.1|FL148341
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211425943|gb|FL148318.1|FL148318
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211428535|gb|FL148329.1|FL148329
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|87152912|gb|DY397701.1|DY397701
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|116813589|gb|EC856040.1|EC856040
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211425942|gb|FL148317.1|FL148317
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGASSTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
EST: gi|211425944|gb|FL148319.1|FL148319
EST:     TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAG                         ATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC
genomic: TGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCC

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), 49 (downstream exon)
Score: 292

TTCCGGCGAAGGGTTTCGGACAGAGAAGATGGCGACGGCGGCGGCAGGGTTGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

TTCCGGCGAAGGGTTTCGGACAGAGAAGATGGCGACGGCGGCGGCAGGGTTGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

TTCCGGCGAAGGGTTTCGGACAGAGAAGATGGCGACGGCGGCGGCAGGGTTGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

TTCCGGCGAAGGGTTTCGGACAGAGAAGATGGCGACGGCGGCGGCAGGGTTGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtcta ... gtctgcgcagATACGGGCGCACGAGGTGGCGATCGCGGAGCTAGACAACCTGAATCCCTCCCGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCGGCGAAGGGTTTCGGACAGAGAAGATGGCGACGGCGGCGGCAGGGTTGGCTCCGGCAAAGGAGGTGGTGGAGAAGAAGGTGGAACTCCTGAAGGAGgtattgtctacctccccatacttcgacacctctatttttgtttcgtgtagttctccacgcaagcttcctgctactgttctccgaattcggctggtggatgagagaaataatttgccgcatggatttggtttggtctgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG