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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGAGCTGCTGCTGGAACCGTCAGGCCGTGAAGAGCCTGCGGTTCGATCTGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctgtggattctttgatccgagacccatcccctatctctctctctctctcctatgggcgcggctttcgcccgattatcgggaggtattgtattt...

Basic information

species Zea mays
transcript GRMZM2G138676_T02
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|211152149|gb|FL424959.1|FL424959
EST:     TGCAAGAGCTCCTCGTCGATCTCTTCTTCTCTGCGAGGTTTCGGTCTGAG                         TTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
genomic: TGCAAGAGCTCCTCGTCGA--TC-TCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
EST: gi|71312508|gb|DR792787.1|DR792787
EST:     TGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAG                         TTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
genomic: TGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
EST: gi|211140437|gb|FL390026.1|FL390026
EST:     TGCAAGAGCTCCTCGTCGATCTCTTCTTCTCTGCGAGGTTTCGGTCTGAG                         TTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCNTGCT
genomic: TGCAAGAGCTCCTCGTCGATCTCTTCT-CT--GCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
EST: gi|211215298|gb|FL416186.1|FL416186
EST:     TGCAAGANCTCCTCGTCGATCTCTTCTTCTCTGCGAGGTTTCGGTCTGAG                         TTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
genomic: TGCAAGAGCTCCTCGTCGA--TC-TCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
EST: gi|89764128|gb|DY691048.1|DY691048
EST:     TGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAG                         TTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
genomic: TGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
EST: gi|91050634|gb|EB161052.1|EB161052
EST:     TGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAG                         TTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT
genomic: TGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCT

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: 39 (upstream exon), 49 (downstream exon)
Score: 190

CCGGAGCTGCTGCTGGAACCGTCAGGCCGTGAAGAGCCTGCGGTTCGATCTGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCTGGTGTTGGGAGCTCCTCGAGGCCAGCTAATGGATTCAAGGGGGCAGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

CCGGAGCTGCTGCTGGAACCGTCAGGCCGTGAAGAGCCTGCGGTTCGATCTGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCTGGTGTTGGGAGCTCCTCGAGGCCAGCTAATGGATTCAAGGGGGCAGCCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 102

CCGGAGCTGCTGCTGGAACCGTCAGGCCGTGAAGAGCCTGCGGTTCGATCTGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCTGGTGTTGGGAGCTCCTCGAGGCCAGCTAATGGATTCAAGGGGGCAGCCA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 160

CCGGAGCTGCTGCTGGAACCGTCAGGCCGTGAAGAGCCTGCGGTTCGATCTGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctg ... gccttaccagTTACCACATTGCTGGAGTGGAGGTATGGCGTATTCTGGACAAAGGCATGCTGGTGTTGGGAGCTCCTCGAGGCCAGCTAATGGATTCAAGGGGGCAGCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGAGCTGCTGCTGGAACCGTCAGGCCGTGAAGAGCCTGCGGTTCGATCTGCTGCAAGAGCTCCTCGTCGATCTCTTCTCTGCGAGGTTTCGGTCTGAGgtactggctgtggattctttgatccgagacccatcccctatctctctctctctctcctatgggcgcggctttcgcccgattatcgggaggtattgtattt

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC