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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCGTCCCGATCTCGCCGCCTGCCCGCCGCGCCCTATTACCGCCATGGAGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcgcgcttatccgcctctcgcaaatcgcgatccatctaagcacccgtaagcgtaagcgtggacagggattgccgtgggctctgaatctctgat...

Basic information

species Zea mays
transcript GRMZM2G104166_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104166_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g45670.1 (Oryza sativa), 5'ss of exon 1
GTCTCGTCCCGA--TCTCGCCGCCTGCCCGCCGCGCCCTATTACCGCCATGGAGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcgcgcttatccgcctctcgcaaatcgcgatcc-atctaagcacccgtaa-gcgtaagcgtggacagggattgc-cgtgggctctgaatctctgat
  | || | ||   | | ||  || |   | ||    |      |||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||| |  ||| | |  |||| ||||   |   | |   |||  | | || ||   |   |    | |   |   | |||||| |    |   ||  ||  ||  
AGCGCGCCGCGGCTTTTTGCGTCCGGAGAGGCGGAGACGG--GGCGCCATGGAGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGAGCAGGTCTCCCGCCAGgtga--cgctctcccatccccctcgatctctttgaactcctgtgttagtacggttctcgatcgatccgagtttgtgattgcgcaaccggggtgggtcgatgt-
















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|93012221|gb|EB637741.1|EB637741
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|91056507|gb|EB166925.1|EB166925
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|50336720|gb|CO531846.1|CO531846
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|148970807|gb|EE021570.2|EE021570
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|91873694|gb|EB403651.1|EB403651
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211195883|gb|FL115001.1|FL115001
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211304270|gb|FL115007.1|FL115007
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAG
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAG
EST: gi|211195880|gb|FL114998.1|FL114998
EST:     AGGCGCTGTGGAAGCAGGCCTTCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211304267|gb|FL115004.1|FL115004
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|148996413|gb|EE035708.2|EE035708
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211195879|gb|FL114997.1|FL114997
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGTCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211304269|gb|FL115006.1|FL115006
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|74236878|gb|DT644792.1|DT644792
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211195882|gb|FL115000.1|FL115000
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211195881|gb|FL114999.1|FL114999
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|76283090|gb|DV022658.1|DV022658
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|76927135|gb|DV171161.1|DV171161
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211304266|gb|FL115003.1|FL115003
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|37424980|gb|CF650224.1|CF650224
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|148981761|gb|EE027867.2|EE027867
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211304268|gb|FL115005.1|FL115005
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|33466753|gb|CF243802.1|CF243802
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
EST: gi|211195884|gb|FL115002.1|FL115002
EST:     AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAG                         GGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT
genomic: AGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcg ... accactgcagGGTGTGTTCAAGCAGTTTGGCTACGGGAATTCTGATAATGCGTTTACAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTCGTCCCGATCTCGCCGCCTGCCCGCCGCGCCCTATTACCGCCATGGAGGCGCTGTGGAAGCAGGCCTCCAGGCTCAAGGACCAGGTCTCTCGGCAGgtcagtcgcgcgcttatccgcctctcgcaaatcgcgatccatctaagcacccgtaagcgtaagcgtggacagggattgccgtgggctctgaatctctgat

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