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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctcacatatgcttcgcttaaaatatcatcttcgtttagactactgatcgggtctcatcttttatcagcttcttaccacgacactgtttcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTCGGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCAATGCAAA

Basic information

species Zea mays
transcript GRMZM2G048277_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 3
aagctcacatatgcttcgcttaaaatatcatcttcgtttagactactgatcgg--gtctcatcttttatcagcttcttaccacgacactgtttcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTC-GGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCA-ATGCAAA
 |  ||  |  |  || || |  | | | |||  | |||||| || | ||||   | |||||| || | ||| |        |     |  ||    | |||||| ||||| ||||| |||||||| |||||||||||||||||||| |      || ||||||       ||| | ||||  | ||  ||| ||| ||||   
-acttctaaattatttagcctgcactgttatcacc-tttagattattaatcgcctgcctcatcattaaccagttaacatgatcattgtttgtttacattcagGCATGGGTACCACTTCATCCTCTGTGAAGGAAGGAAGAACTGATCAGTCTGCTTCAGGTTGGAACAGAAGCACC-TCAGTCTATACAAGATGCAGATGCCT-
















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|32828122|gb|CD967800.1|CD967800
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|33096518|gb|CF056512.1|CF056512
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGCATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|18177877|gb|BM379087.1|BM379087
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|211061968|gb|FL461781.1|FL461781
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|51592806|gb|CV071952.1|CV071952
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|60337887|gb|DN204860.1|DN204860
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|32827994|gb|CD967672.1|CD967672
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|32823460|gb|CD963182.1|CD963182
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|76283286|gb|DV022854.1|DV022854
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|211106101|gb|FL459223.1|FL459223
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCMCCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|110524567|gb|EE028751.1|EE028751
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTTTGCGAAGGAAGGAAGAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|67017951|gb|CO446700.1|CO446700
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATCCTCTGCGAAAGAAGGA-GAACTGATCTGGAAA
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAA
EST: gi|166410049|gb|EG271119.1|EG271119
EST:     GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCAC                         GCACGGGTATCACTTTATC
genomic: GTTGCTTTCAACACACCTGAGGGAACTGTTAGCGCACCATTCAAGTCCACgtatgccttt ... tcctgtgcagGCACGGGTATCACTTTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatcgggtctcatcttttatcagcttcttaccacgacactgtttcctgtgcagGCACGGGTATCACTTTATCCTCTGCGAAGGAAGGAAGAACTGATCTGGAAATGTCGGTTGGGGAGACTGCATCATCAGGTTGTATGAGACGCAATGCAAA
                          ttcttac  putative branch site (score: 2)
                                        ctgtttcct  putative PPT
             atcttttat  TA-rich tract