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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAAATTTGCTCATGTTACATTCAGTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataagttttccttttggcgaaagaatcctttcgcaagaacattcattgtaacattgaagtattgtataagcttttcctggtattgttttag

Basic information

species Zea mays
transcript GRMZM2G071441_T01
intron # 26
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|19058849|gb|BM737516.1|BM737516
EST:     GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
EST: gi|32865867|gb|CF005549.1|CF005549
EST:     GTAAGCCAGAATACCTCCAAGATTCAGANNNNNNNATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
EST: gi|32834007|gb|CD973685.1|CD973685
EST:     GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
EST: gi|67023760|gb|CO452509.1|CO452509
EST:     GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
EST: gi|37382211|gb|CF628041.1|CF628041
EST:     GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
EST: gi|32940265|gb|CF045084.1|CF045084
EST:     GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
EST: gi|211172393|gb|FL129172.1|FL129172
EST:     GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
EST: gi|91050276|gb|EB160694.1|EB160694
EST:     GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
EST: gi|88750432|gb|DY534573.1|DY534573
EST:     GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCAT                         AAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT
genomic: GTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCAT

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: 47 (upstream exon), 49 (downstream exon)
Score: 220

TGGAAATTTGCTCATGTTACATTCAGTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCATACAGCCACCACCCCAAAAAGGTCCTACTTAGGCAACAACCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 105

TGGAAATTTGCTCATGTTACATTCAGTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCATACAGCCACCACCCCAAAAAGGTCCTACTTAGGCAACAACCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 125

TGGAAATTTGCTCATGTTACATTCAGTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCATACAGCCACCACCCCAAAAAGGTCCTACTTAGGCAACAACCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 165

TGGAAATTTGCTCATGTTACATTCAGTAAGCCAGAATACCTCCAAGATTCAGATATTGTAATGAACAGATTCCATgtgagataag ... attgttttagAAACAGAGACCTGTTTATGGAGGTTGGGAACAACACCTTGGATTGGAGCATACAGCCACCACCCCAAAAAGGTCCTACTTAGGCAACAACCAG