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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatagatcccaagacccaaagctatatactgaaaaccatttatccttgtcatttgaccactgagcgtttgcattttgtttgtgtttcttatcatccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCACCTGTACAGCAGAAGATAGCGAGGCCTAGCTTTTTACCATTACCAGTAG

Basic information

species Zea mays
transcript GRMZM2G123537_T02
intron # 9
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|47961753|gb|CN844462.1|CN844462
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|211232325|gb|FK959922.1|FK959922
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|32867178|gb|CF006860.1|CF006860
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|89760633|gb|DY688965.1|DY688965
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AAGGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|24763548|gb|CA398720.1|CA398720
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60394394|gb|DN227264.1|DN227264
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60355644|gb|DN222617.1|DN222617
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|113702621|gb|EE680125.1|EE680125
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60355743|gb|DN222716.1|DN222716
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60398356|gb|DN231172.1|DN231172
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60399207|gb|DN232021.1|DN232021
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
EST: gi|60357180|gb|DN224153.1|DN224153
EST:     CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAG                         AACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA
genomic: CTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCA

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), 45 (downstream exon)
Score: 200

TTGATTCTTTCCCGTATCAAGGTCCACTTGAATGCACTGAAAAGGTACACCTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCACCTGTACAGCAGAAGATAGCGAGGCCTAGCTTTTTACCATTACCAGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

TTGATTCTTTCCCGTATCAAGGTCCACTTGAATGCACTGAAAAGGTACACCTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCACCTGTACAGCAGAAGATAGCGAGGCCTAGCTTTTTACCATTACCAGTAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 241

TTGATTCTTTCCCGTATCAAGGTCCACTTGAATGCACTGAAAAGGTACACCTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCACCTGTACAGCAGAAGATAGCGAGGCCTAGCTTTTTACCATTACCAGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 496

TTGATTCTTTCCCGTATCAAGGTCCACTTGAATGCACTGAAAAGGTACACCTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagat ... tccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCACCTGTACAGCAGAAGATAGCGAGGCCTAGCTTTTTACCATTACCAGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttgaccactgagcgtttgcattttgtttgtgtttcttatcatccttttcagAACGGCGCATTGGCGCACTACCCTCCTGCTGAGATGGCAATGGTTAGGTCACCTGTACAGCAGAAGATAGCGAGGCCTAGCTTTTTACCATTACCAGTAG
  atttgac  putative branch site (score: 496)
                                   tttcttatcatccttt  putative PPT
                       attttgttt  TA-rich tract