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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcactctttttttttgttctttgttttcgctatcatgtgtacaggcctgatcctcatttttccatagtctgttactgaccatatctttgctatgttaccctgctttactgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAATGTCATTCAACATGAATTACAAGGACACTGGTCTTTTTGGTGTCTATGCT

Basic information

species Zea mays
transcript GRMZM2G091563_T01
intron # 4
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|60337054|gb|DN204027.1|DN204027
EST:     TCAATGCTTGGTTCATGGAACAAGAGTACTGGTGGAGGAAAGCACATGGG                         TTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAAT
genomic: TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAAT
EST: gi|32920213|gb|CF025025.1|CF025025
EST:     TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGG                         TTCGGAGCTTGT
genomic: TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGT
EST: gi|32920952|gb|CF025764.1|CF025764
EST:     TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGG                         TTCGGAGCTTGT
genomic: TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGT
EST: gi|32922064|gb|CF026876.1|CF026876
EST:     TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGG                         TTCGGAGCTTGT
genomic: TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGT
EST: gi|60355748|gb|DN222721.1|DN222721
EST:     TCAATGCTTGGTTCATGGAACAAGAGTACTGGTGGAGGAAAGCACATGGG                         TTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAAT
genomic: TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAAT
EST: gi|32920826|gb|CF025638.1|CF025638
EST:     TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGG                         TTCGGAGCTTGT
genomic: TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGT
EST: gi|32922080|gb|CF026892.1|CF026892
EST:     TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGG                         TTCGGAGCTTGT
genomic: TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGT
EST: gi|5895629|gb|AW036875.1|AW036875
EST:     TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGG                         TTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAAT
genomic: TCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAAT

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: 277

ATGGAGCATCATGGGTAGATCCTGATTCTGTTGCACTGATGGTTATGCAATCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAATGTCATTCAACATGAATTACAAGGACACTGGTCTTTTTGGTGTCTATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

ATGGAGCATCATGGGTAGATCCTGATTCTGTTGCACTGATGGTTATGCAATCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAATGTCATTCAACATGAATTACAAGGACACTGGTCTTTTTGGTGTCTATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

ATGGAGCATCATGGGTAGATCCTGATTCTGTTGCACTGATGGTTATGCAATCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAATGTCATTCAACATGAATTACAAGGACACTGGTCTTTTTGGTGTCTATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

ATGGAGCATCATGGGTAGATCCTGATTCTGTTGCACTGATGGTTATGCAATCAATGCTTGGTTCATGGAACAAGAGTGCTGGTGGAGGAAAGCACATGGGgtaagttcac ... ctgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAATGTCATTCAACATGAATTACAAGGACACTGGTCTTTTTGGTGTCTATGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagtctgttactgaccatatctttgctatgttaccctgctttactgtttacagTTCGGAGCTTGTACAGAAAGCAGCAATCAATGACATTGCTGAGAGTGTAATGTCATTCAACATGAATTACAAGGACACTGGTCTTTTTGGTGTCTATGCT
          tactgac  putative branch site (score: 365)
                                        ctttact  putative PPT
                  atatcttt  TA-rich tract