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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAATATGTTGACATGGTGAAGACCGGTATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgatcttttattttgaacagtaggaagttattaactagtttccatgatagacaatcagccaacaatgatgaggctattaactagtttctatcgc...

Basic information

species Zea mays
transcript GRMZM2G111477_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111477_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 17
GTGAATATGTTGACATGGTGAAGACCGGTATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaact----gatcttttattttgaacagtaggaagtt--attaactagtt--tccatgatagacaatcagccaacaatgatgaggctattaactagtttctatcgc---------------------------------------------------------------------------------
|||||||||| |||||||||||| | |||||||||||||| ||||| || ||||||||||| |||||||||||||| |||||| ||      |   |  || ||  |  |||    ||  ||||| | |||  || |  || |   ||   |  |  |  |     ||  |  || ||   |||  |                                                                                 
GTGAATATGTGGACATGGTGAAGGCTGGTATCATTGACCCACTAAAAGTGATCAGAACTGCCTTGGTGGATGCTGCAAGgtaagctctcaagttcatggttctgtgctttagttctttacattaaattgttgatcaaacatgggtgatacactga--agcacccacctcatcccttgtgcttatttcggtttttgatctgaaatttttcacccatttaacgttacttttggctcttgcgggttcttacaagttgtttgccttctgcag
















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|76020164|gb|DT947334.1|DT947334
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|74236027|gb|DT643941.1|DT643941
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|76020163|gb|DT947333.1|DT947333
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|113703063|gb|EE680567.1|EE680567
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|67018599|gb|CO447348.1|CO447348
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|74236026|gb|DT643940.1|DT643940
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|15057239|gb|BI361211.1|BI361211
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|5108264|gb|AI739977.1|AI739977
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|60394542|gb|DN227412.1|DN227412
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|37400119|gb|CF637406.1|CF637406
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|113607172|gb|DW776759.1|DW776759
EST:     CTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: CTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|211121936|gb|FL439136.1|FL439136
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|60397850|gb|DN230666.1|DN230666
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|78119934|gb|DV538318.1|DV538318
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
EST: gi|113616752|gb|DW782955.1|DW782955
EST:     CTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGACTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCA
genomic: CTAAAGGTTATCAGAACTGCTTTGGTGGATGCTG-CTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCA
EST: gi|60348034|gb|DN215007.1|DN215007
EST:     ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA
genomic: ATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgat ... cattttgcagTGTGTCGTCCCTGATGACAACCACGGAATCCATAATTGTAGAGATTCCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAATATGTTGACATGGTGAAGACCGGTATCATTGACCCGCTAAAGGTTATCAGAACTGCTTTGGTGGATGCTGCTAGgtaaactgatcttttattttgaacagtaggaagttattaactagtttccatgatagacaatcagccaacaatgatgaggctattaactagtttctatcgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT