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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaatcgacttccaagtttaaactgcagagatgcaacttcattgaaggaaaaaaactatagagatcaagaaatagtagtaatctgaacaaacctttag

Basic information

species Zea mays
transcript GRMZM2G147256_T02
intron # 3
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|71299596|gb|DR785811.1|DR785811
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|76912287|gb|DV164658.1|DV164658
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|101397910|gb|EB820832.1|EB820832
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|149098292|gb|EE184260.2|EE184260
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|89763649|gb|DY690753.1|DY690753
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|94474055|gb|EB703013.1|EB703013
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|84970143|gb|DW468493.1|DW468493
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|78124407|gb|DV542791.1|DV542791
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|93284471|gb|EB676735.1|EB676735
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|74236569|gb|DT644483.1|DT644483
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|78119582|gb|DV537966.1|DV537966
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|50335970|gb|CO531096.1|CO531096
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|78124376|gb|DV542760.1|DV542760
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|71758972|gb|DR956909.1|DR956909
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
EST: gi|14245232|gb|BG873814.1|BG873814
EST:     GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG                         GCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT
genomic: GCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTT

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), 41 (downstream exon)
Score: 25

GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTTCTTTGTGCTGCTGCTCATGTTGCCGTTCGTGACACTGTGGGAAAGCTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 97

GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTTCTTTGTGCTGCTGCTCATGTTGCCGTTCGTGACACTGTGGGAAAGCTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 31

GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTTCTTTGTGCTGCTGCTCATGTTGCCGTTCGTGACACTGTGGGAAAGCTTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 57

GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAGgtcagatcaa ... aaacctttagGCCAGAATTCTCCGGAAGACCCTAGGCGGTGGAATGAGACAGGTGGGAGTTCTTTGTGCTGCTGCTCATGTTGCCGTTCGTGACACTGTGGGAAAGCTTG