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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccaccgtccccggtcacccagatctgtcgctttagtttcatttcgatcgcgatgctgagagattttggggggccttgtgcgcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGGACGGTGGACTCGCAGGAGTCGCTTGGCGGCGGCGTCACTGTGCTCGTCA

Basic information

species Zea mays
transcript GRMZM2G091995_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091995_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g29480.1 (Oryza sativa), 3'ss of exon 2
--------------------------gtga-gccaccgtccccggtcacccagatctgtcgctttagtttca---tttcgatcgcgatgctgaga--gattttggggggcctt--gtgcgcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGGACGGTGGACTCGCAGGAGTCGCTTGGCGGCGGCGTCACTGTGCTCGTCA
                          | |  ||| |    |   | |  |||  |||| || |||  ||| |   ||  | | | |||| ||| |   |  | ||||||  ||  ||| |  |  |||||| |||  ||||||||| ||||  |||||| ||||    |||||||||| ||||||||| |||||||||||||| |||||||||||||| ||||| ||||
gtcagcccccgccgcctccagatctggcgccgccgcgaggcggaggcctccatttctgacgatttttttttaattttctggttgggatggtgacacgaagatgggggggtttttggtgtggttccgcagGCGATCAACGAGAAGATCATGGCCATGGACATGTCGCGGGCGGAGATCAAGACGGTGGATTCGCAGGAGTCGCTCGGCGGCGGCGTCACCGTGCTTGTCA
















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|71766908|gb|DR964845.1|DR964845
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|71768664|gb|DR966601.1|DR966601
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|37425130|gb|CF650301.1|CF650301
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|149078936|gb|EE167772.2|EE167772
EST:     CGCATCCGCCGCCGGAGCCCGCCGG-ATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CGCATCCGCCGCCGGAGCC-GCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|50336246|gb|CO531372.1|CO531372
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|148964753|gb|EC906012.2|EC906012
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|94473274|gb|EB702232.1|EB702232
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211393824|gb|FK983472.1|FK983472
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211396446|gb|FK983487.1|FK983487
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|148956890|gb|EC902811.2|EC902811
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211396444|gb|FK983485.1|FK983485
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211396441|gb|FK983482.1|FK983482
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211393820|gb|FK983468.1|FK983468
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211393826|gb|FK983474.1|FK983474
EST:     CCGCATCCGCCGCCGGAGCCGCCGGSATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|149047149|gb|EE048155.2|EE048155
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211393819|gb|FK983467.1|FK983467
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|148959103|gb|EE010585.2|EE010585
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211396445|gb|FK983486.1|FK983486
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAAATGGAGATGGACGTGTCAAAAGCGGAGATCAG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAA-TGGAGATGGACGTGTCAAAAGCGGAGATCAG
EST: gi|211396437|gb|FK983478.1|FK983478
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|148957059|gb|EC903023.2|EC903023
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211393821|gb|FK983469.1|FK983469
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|91055356|gb|EB165774.1|EB165774
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
EST: gi|211393825|gb|FK983473.1|FK983473
EST:     CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAG                         GCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG
genomic: CCGCATCCGCCGCCGGAGCCGCCGGCATGGACTCCGTCACCACTATGGAGgtgagccacc ... gcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatttcgatcgcgatgctgagagattttggggggccttgtgcgcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGGACGGTGGACTCGCAGGAGTCGCTTGGCGGCGGCGTCACTGTGCTCGTCA
                        agatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccaccgtccccggtcacccagatctgtcgctttagtttcatttcgatcgcgatgctgagagattttggggggccttgtgcgcctatgcagGCAATCGGCGAGAAGATAATGGAGATGGACGTGTCAAAAGCGGAGATCAGGACGGTGGACTCGCAGGAGTCGCTTGGCGGCGGCGTCACTGTGCTCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA