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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactatatggtgcctgagtcttgcatgaggttgacaaattcttttgttcactaactctttgcctgctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCCCCACTTGCAGCCAGTACCATGTATGGCTATCAAGGGCAGAGTCATCAGG

Basic information

species Zea mays
transcript GRMZM2G163888_T01
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|32846535|gb|CD986216.1|CD986216
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|211462558|gb|FL333208.1|FL333208
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGAGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|101394451|gb|EB819160.1|EB819160
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|32941317|gb|CF046136.1|CF046136
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|91048810|gb|EB159228.1|EB159228
EST:     TTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: TTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|149061080|gb|EE157337.2|EE157337
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|149013572|gb|EE043052.2|EE043052
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|30306548|gb|CD001221.1|CD001221
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|30705282|gb|CD058732.1|CD058732
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|60396154|gb|DN229023.1|DN229023
EST:     GTCCCCTTCACATTTCAAAGATGGAAATCAATTTATTTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: GT-CCCTTCACATTTCAAAGATGGAAATCAATTTA-TTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|30088189|gb|CB886394.1|CB886394
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|95107690|gb|EB739919.1|EB739919
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGC
EST: gi|60342207|gb|DN209180.1|DN209180
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGAGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|87157453|gb|DY402242.1|DY402242
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|211310430|gb|FL459507.1|FL459507
EST:     GAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGAGCTAGTTCACGA-GGATGCCC
genomic: GAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|211470005|gb|FL327953.1|FL327953
EST:     TTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGAGCTAGTTCACGAGGGATGCCC
genomic: TTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|71444780|gb|DR825830.1|DR825830
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|30705899|gb|CD058963.1|CD058963
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
EST: gi|30087800|gb|CB886006.1|CB886006
EST:     CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAG                         AATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC
genomic: CGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCC

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), 41 (downstream exon)
Score: 152

TCTGAATCAAAGCACAGCAGCAGCAACAACAACTCTTGGGTTTGATGGGACGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCCCCACTTGCAGCCAGTACCATGTATGGCTATCAAGGGCAGAGTCATCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

TCTGAATCAAAGCACAGCAGCAGCAACAACAACTCTTGGGTTTGATGGGACGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCCCCACTTGCAGCCAGTACCATGTATGGCTATCAAGGGCAGAGTCATCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

TCTGAATCAAAGCACAGCAGCAGCAACAACAACTCTTGGGTTTGATGGGACGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCCCCACTTGCAGCCAGTACCATGTATGGCTATCAAGGGCAGAGTCATCAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 116

TCTGAATCAAAGCACAGCAGCAGCAACAACAACTCTTGGGTTTGATGGGACGGTCCCTTCACATTTCAAAGATGGAAATCAATTTATTTCTCTTCAGCAGgtaaactata ... ctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCCCCACTTGCAGCCAGTACCATGTATGGCTATCAAGGGCAGAGTCATCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatgaggttgacaaattcttttgttcactaactctttgcctgctgctgacagAATGAGAACCCTGCAATGTGGATGCATGGTGCTAGTTCACGAGGGATGCCCCCACTTGCAGCCAGTACCATGTATGGCTATCAAGGGCAGAGTCATCAGG
                            cactaac  putative branch site (score: 116)
               aaattctttt  TA-rich tract