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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttacagagactcaatcttactgccatatttatatggttcaaaattactgcatcgctcattgctccctgactatacgaagaatctgtttctttagg...

Basic information

species Zea mays
transcript GRMZM5G824831_T08
intron # 11
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|18181390|gb|BM382600.1|BM382600
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|211269953|gb|FL444406.1|FL444406
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|6952542|gb|AW424610.1|AW424610
EST:     TCCTCCAACAACATTGAAATCGCAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTCTAAGCCCAG
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAG
EST: gi|148973074|gb|EE024136.2|EE024136
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|78112696|gb|DV531090.1|DV531090
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTTTTGGAAGAGGGGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|5268558|gb|AI770522.1|AI770522
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGCTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|211149323|gb|FL312581.1|FL312581
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|32830197|gb|CD969875.1|CD969875
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|6194486|gb|AW146590.1|AW146590
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|67024880|gb|CO453629.1|CO453629
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
EST: gi|211321302|gb|FL273340.1|FL273340
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAA                         AGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGC

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: 53

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 16

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 15

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 13

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttaca ... caaaatacagAGTTTTAAGCCCAGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGCTGTCTGTTGATGATACTAGTTCAGACAACAATAGCAGCGTCACTTATGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGATCGTGAGTTCAAgtaagttacagagactcaatcttactgccatatttatatggttcaaaattactgcatcgctcattgctccctgactatacgaagaatctgtttctttagg

- - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT