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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCCGAGCCGCGCTGCTCACAAGCGACCGCGTCACGGCCGACGACCCCAGGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacagccgccatcaacagatgtggtggaaatggaacattctcgtgtcaagctgcccttgaagttaccaggagtccaggaattgggacaagtggtt...

Basic information

species Zea mays
transcript GRMZM2G092131_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092131_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g28840.1 (Oryza sativa), 5'ss of exon 2
GCCCCGAGCCGCGCTGCTCACAAGCGACCGCGTCACGGCCGACGACCCCAGGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacagccgccatcaacaga-tgtggtggaaatggaacattctcgtgtcaagctgcc-cttgaagttaccaggagtccaggaattgggacaagtggtt
||| || ||||| |||||||| |||| |||||||| || ||| ||||||||||||||| ||| ||||  |  ||||   ||||||||||||||||| |||||||   ||   |||     |||  |||  | ||| ||        |  ||    | | |   ||| |||     |   ||   |  |  | |  |||||  
GCCGCGCGCCGCCCTGCTCACCAGCGGCCGCGTCATGGACGATGACCCCAGGATCGCCTCCTCCGTCGCCAGCCACCTCCCCCGCCTCTCCTCCGTCCAGgtaatttcatatgcctatgtcaggctgtcttcgaattgacttgagttgttggatggtttcgatttggagtgcattgctctcgttgtttccgcaacagtgg--
















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|211084846|gb|FL280290.1|FL280290
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|89252045|gb|DY623831.1|DY623831
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|91048511|gb|EB158929.1|EB158929
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|149077854|gb|EE166581.2|EE166581
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|211084844|gb|FL280288.1|FL280288
EST:     GATCGCCGCCTGCGTCASSGCCCACAAGCCCCGCCTSSKCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCT-CCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|101390617|gb|EB817243.1|EB817243
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|93015506|gb|EB641026.1|EB641026
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|76932735|gb|DV173138.1|DV173138
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|101398534|gb|EB821140.1|EB821140
EST:     GGATCGCCGCCCGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|71771111|gb|DR969048.1|DR969048
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|211084842|gb|FL280286.1|FL280286
EST:     GGATCGCCGCCTGCGTSAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|71441696|gb|DR831412.1|DR831412
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|71435233|gb|DR816283.1|DR816283
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|211084845|gb|FL280289.1|FL280289
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
EST: gi|211084843|gb|FL280287.1|FL280287
EST:     GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAG                         ATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC
genomic: GGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacag ... aattttacagATACTCATAGTGTGCTTATTGGCCGAAGTGGGGAAAGGGAGCAACTCTGTC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCCGAGCCGCGCTGCTCACAAGCGACCGCGTCACGGCCGACGACCCCAGGATCGCCGCCTGCGTCAGCGCCCACAAGCCCCGCCTCTCCTCCGTGCAGgtaaacacagccgccatcaacagatgtggtggaaatggaacattctcgtgtcaagctgcccttgaagttaccaggagtccaggaattgggacaagtggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC