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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatcacttgttcaaatcctctttatctgtctaatgaatattactccccatgtctattattttccttcaatactcatacaagtctataaatcttattgtctgtgcctgtttttaacagAGTGATCGGCTGAAGCAAGTCATGGAACATCTTAACACTTTGCATTCGTTATGCGAGGTGCTTGGTGTAGACTTCAAACAAACAGTAAATGAGGTGCACC

Basic information

species Zea mays
transcript GRMZM2G126913_T02
intron # 11
splice site 3'
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|32839865|gb|CD979546.1|CD979546
EST:     GAAAGCTGGAGGAGCTAACGAAAGAGCTGCAATCCCTTCAGAAGGAGAAG                         AGTGATCGGCTGAAGCAAGTCATGGAACATCTTAACACTTTGCATTCATTA
genomic: GAAAGCTGGAGGAGCTAACGAAAGAGCTGCAATCCCTTCAGAAGGAGAAGgttagcatca ... tttttaacagAGTGATCGGCTGAAGCAAGTCATGGAACATCTTAACACTTTGCATTCGTTA




















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: 48 (upstream exon), 47 (downstream exon)
Score: 560

AGATATTGTACCCTTTAGAATTCCTGTGGATCAGTCTGATCTGTCTTTAAGAAAGCTGGAGGAGCTAACGAAAGAGCTGCAATCCCTTCAGAAGGAGAAGgttagcatca ... tttttaacagAGTGATCGGCTGAAGCAAGTCATGGAACATCTTAACACTTTGCATTCGTTATGCGAGGTGCTTGGTGTAGACTTCAAACAAACAGTAAATGAGGTGCACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

AGATATTGTACCCTTTAGAATTCCTGTGGATCAGTCTGATCTGTCTTTAAGAAAGCTGGAGGAGCTAACGAAAGAGCTGCAATCCCTTCAGAAGGAGAAGgttagcatca ... tttttaacagAGTGATCGGCTGAAGCAAGTCATGGAACATCTTAACACTTTGCATTCGTTATGCGAGGTGCTTGGTGTAGACTTCAAACAAACAGTAAATGAGGTGCACC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 105

AGATATTGTACCCTTTAGAATTCCTGTGGATCAGTCTGATCTGTCTTTAAGAAAGCTGGAGGAGCTAACGAAAGAGCTGCAATCCCTTCAGAAGGAGAAGgttagcatca ... tttttaacagAGTGATCGGCTGAAGCAAGTCATGGAACATCTTAACACTTTGCATTCGTTATGCGAGGTGCTTGGTGTAGACTTCAAACAAACAGTAAATGAGGTGCACC


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 81

AGATATTGTACCCTTTAGAATTCCTGTGGATCAGTCTGATCTGTCTTTAAGAAAGCTGGAGGAGCTAACGAAAGAGCTGCAATCCCTTCAGAAGGAGAAGgttagcatca ... tttttaacagAGTGATCGGCTGAAGCAAGTCATGGAACATCTTAACACTTTGCATTCGTTATGCGAGGTGCTTGGTGTAGACTTCAAACAAACAGTAAATGAGGTGCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcaatactcatacaagtctataaatcttattgtctgtgcctgtttttaacagAGTGATCGGCTGAAGCAAGTCATGGAACATCTTAACACTTTGCATTCGTTATGCGAGGTGCTTGGTGTAGACTTCAAACAAACAGTAAATGAGGTGCACC
                                         cctgttttt  CT-rich tract
                   tctataaatcttatt  TA-rich tract