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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacaccctgctctgctctgacagcgccagcggcagcgcctacgccggccattttcggcctgggttgcttgtgtgcgcgcgtggctgaagctgggaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTGAACAGCAAGCACTACACCACCAAGGTCATCTCGGCGGTGGTTGTCGTGG

Basic information

species Zea mays
transcript GRMZM2G055216_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055216_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g39280.1 (Oryza sativa), 3'ss of exon 2
gtacgtacaccctgctctgctctgacagcgccagcggcagcgcctacgccggccattttcggcctgggttgcttgtgtgcgcgcgtggctgaagctgggaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTGAACAGCAAGCACTACACCACCAAGGTCATCTCGGCGGTGGTTGTCGTGG
|||  |  |   |   ||    || |        | | |  |  |      ||| | ||  ||    || |    ||   | |||   |     |||  |||||| ||||||| ||| |||||||||| |||||||| ||| | |||||||||||||| |||||||||||||||||||||||||| || ||||| ||||| |||||||
gtat-tgtatatt-tactaggttgcccat-ttgcctggaatgtttgtatatgccgtcttgtgctcttgt-gtggctgaaggtgcgaaacct---ctgcaaacctgtagATCTCGAAATTGAGCATGATCCCGGTGGTTTGCTTGATGGAATGGGTGCTCAACAGCAAGCACTACACCACCAAGGTTATATCGGCCGTGGTCGTCGTGG
















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|50337879|gb|CO533005.1|CO533005
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|149008482|gb|EE040648.2|EE040648
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|50337628|gb|CO532754.1|CO532754
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|211053522|gb|FL140432.1|FL140432
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|71318582|gb|DR796050.1|DR796050
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAA                         ATCTCCAAACTGAGCATGATTCCCGGTGGTCTGCCTCATGGCATGGGT
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCC-GGTGGTCTGCCTCATGGAATGGGT
EST: gi|211053523|gb|FL140433.1|FL140433
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|91869654|gb|EB400482.1|EB400482
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|211056459|gb|FL140439.1|FL140439
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATG
EST: gi|71314415|gb|DR793832.1|DR793832
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|78082074|gb|DV510486.1|DV510486
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|211053525|gb|FL140435.1|FL140435
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|71436404|gb|DR817454.1|DR817454
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|86466628|gb|DY232998.1|DY232998
EST:     TCACCGGGATGAACCTCAGCCTCGTGCTCAACTCCGTCGGCTTCTACCAT                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|76935918|gb|DV174533.1|DV174533
EST:     TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|149101076|gb|EE187177.2|EE187177
EST:     CACCGGGATGAACCTCAGCCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACTGAGCATGATTCCCGTGGTCTGCCTCATGGAATGGGTGCTG
genomic: CACCGGGATGAACCTCAGCC-TCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTG
EST: gi|211053524|gb|FL140434.1|FL140434
EST:     TCACCGGGATGAACCTYAGCCTCATGCTCAACTCCGTCGGCTTCTACCAG                         ATCTCCAAACT
genomic: TCACCGGGATGAACCTCAGCCTCATGCTCAACTCCGTCGGCTTCTACCAGgtacgtacac ... gaacctgcagATCTCCAAACT

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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacaccctgctctgctctgacagcgccagcggcagcgcctacgccggccattttcggcctgggttgcttgtgtgcgcgcgtggctgaagctgggaacctgcagATCTCCAAACTGAGCATGATTCCGGTGGTCTGCCTCATGGAATGGGTGCTGAACAGCAAGCACTACACCACCAAGGTCATCTCGGCGGTGGTTGTCGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG