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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcgcaacacgtgttttcgaatcttgttggcatcggaactgcatgccagttttgctaacacattctcctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAAATGTTTCTCACCGAGGGTGACATCGAGGTTCTCGGTGTATAAGCATGAG

Basic information

species Zea mays
transcript GRMZM2G042398_T01
intron # 13
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|16925826|gb|BM078894.1|BM078894
EST:     AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG                         CGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
genomic: AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
EST: gi|32937233|gb|CF042052.1|CF042052
EST:     AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG                         CGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
genomic: AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
EST: gi|18165495|gb|BM335334.1|BM335334
EST:     AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG                         CGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
genomic: AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
EST: gi|211031439|gb|FL127271.1|FL127271
EST:     AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG                         CGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
genomic: AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
EST: gi|18165055|gb|BM334900.1|BM334900
EST:     AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG                         CGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
genomic: AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
EST: gi|60395442|gb|DN228312.1|DN228312
EST:     AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG                         CGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
genomic: AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
EST: gi|211475864|gb|FL467329.1|FL467329
EST:     AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG                         CGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
genomic: AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
EST: gi|18164178|gb|BM334017.1|BM334017
EST:     AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG                         CGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA
genomic: AAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAA

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: 46 (upstream exon), 47 (downstream exon)
Score: 44

GTACACTGTCACAAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAAATGTTTCTCACCGAGGGTGACATCGAGGTTCTCGGTGTATAAGCATGAG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 23

GTACACTGTCACAAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAAATGTTTCTCACCGAGGGTGACATCGAGGTTCTCGGTGTATAAGCATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 25

GTACACTGTCACAAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAAATGTTTCTCACCGAGGGTGACATCGAGGTTCTCGGTGTATAAGCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GTACACTGTCACAAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAGgtactgcgca ... cctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAAATGTTTCTCACCGAGGGTGACATCGAGGTTCTCGGTGTATAAGCATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgttggcatcggaactgcatgccagttttgctaacacattctcctttcacagCGAGGCCAACCGCCTACCCAACGAAGAGCCAGCAACGCAAACAGAGGGAAAATGTTTCTCACCGAGGGTGACATCGAGGTTCTCGGTGTATAAGCATGAG
                               tgctaac  putative branch site (score: 65)
                                     cacattctcctttc  CT-rich tract