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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttttgaaacggggacaagtgatctatttgctcttcttgcactttctatgtttccacaatttttaagaatattttggaagcaagttaatatgcgcagaatttgtgcgcaatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCCAGGAGTGAAATTTTCGCTACATCCTAGCTAGACCAGGACTCGCGATGTA

Basic information

species Zea mays
transcript GRMZM2G060896_T02
intron # 11
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|211473095|gb|FL459190.1|FL459190
EST:     GAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: GAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|37387068|gb|CF630726.1|CF630726
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|5819350|gb|AI987556.1|AI987556
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|5714138|gb|AI944123.1|AI944123
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|45567480|gb|CK985592.1|CK985592
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|5847113|gb|AW000192.1|AW000192
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|40303182|gb|CK347569.1|CK347569
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|37394872|gb|CF634714.1|CF634714
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|6056688|gb|AW091093.1|AW091093
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|5597203|gb|AI891196.1|AI891196
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|37390214|gb|CF632335.1|CF632335
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|6095484|gb|AW120151.1|AW120151
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|71305268|gb|DR788768.1|DR788768
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|6022576|gb|AW067388.1|AW067388
EST:     CGACCTTGGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|32850727|gb|CD990408.1|CD990408
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACAGCGGCGGCACCACTGAAGTTGACTCTTGCATCT
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|5525664|gb|AI861557.1|AI861557
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCCCTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|37389864|gb|CF632156.1|CF632156
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
EST: gi|40303414|gb|CK347801.1|CK347801
EST:     CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACA                         GAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC
genomic: CGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCC

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), 49 (downstream exon)
Score: 60

ATGCATAGGGCAGCATTTGTTCTCCCGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCCAGGAGTGAAATTTTCGCTACATCCTAGCTAGACCAGGACTCGCGATGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

ATGCATAGGGCAGCATTTGTTCTCCCGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCCAGGAGTGAAATTTTCGCTACATCCTAGCTAGACCAGGACTCGCGATGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

ATGCATAGGGCAGCATTTGTTCTCCCGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCCAGGAGTGAAATTTTCGCTACATCCTAGCTAGACCAGGACTCGCGATGTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 85

ATGCATAGGGCAGCATTTGTTCTCCCGACCTTTGCAAGGAGAGAGCTAGAAGCATATTGCGTTTCCACTGAAACAgtaagttctt ... aatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCCAGGAGTGAAATTTTCGCTACATCCTAGCTAGACCAGGACTCGCGATGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagaatattttggaagcaagttaatatgcgcagaatttgtgcgcaatgtcacagGAGCAAGCGGAGGAAACACCGGCGGCACCACTGAAGTTGACTCTTGCATCCAGGAGTGAAATTTTCGCTACATCCTAGCTAGACCAGGACTCGCGATGTA
                   agttaat  putative branch site (score: 85)
                  aagttaatat  TA-rich tract