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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttctttttgacatattttcaacactaattttggcggcatcgtcatgaaagaatccttttatttatatacgaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAAATTTAAGAAACTGTATGATGACCTCACCACTGGTTTCCGCAATCTCGAA

Basic information

species Zea mays
transcript GRMZM2G128877_T04
intron # 2
splice site 3'
intron type U2

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|67018748|gb|CO447497.1|CO447497
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|6827260|gb|AW330903.1|AW330903
EST:     GTTTGGGCGATCT-TTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGGTCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: GTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|60291764|gb|DN190003.1|DN190003
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|5871663|gb|AW018134.1|AW018134
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|4630580|gb|AI621454.1|AI621454
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|32833833|gb|CD973511.1|CD973511
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|5770168|gb|AI973342.1|AI973342
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|33103191|gb|CF063151.1|CF063151
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|5804554|gb|AI979524.1|AI979524
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|33103198|gb|CF063158.1|CF063158
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|4646572|gb|AI491316.2|AI491316
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|4572998|gb|AI586647.1|AI586647
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|33101606|gb|CF061566.1|CF061566
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|33095505|gb|CF055499.1|CF055499
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCCAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|32929306|gb|CF034118.1|CF034118
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|67018094|gb|CO446843.1|CO446843
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|32835087|gb|CD974765.1|CD974765
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|32928630|gb|CF033442.1|CF033442
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|32846470|gb|CD986151.1|CD986151
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGC                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|61236472|gb|DN586224.1|DN586224
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
EST: gi|32940788|gb|CF045607.1|CF045607
EST:     ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT                         ATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA
genomic: ACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGTgtaagtattt ... gaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttggcggcatcgtcatgaaagaatccttttatttatatacgaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAAATTTAAGAAACTGTATGATGACCTCACCACTGGTTTCCGCAATCTCGAA
 cactaat  putative branch site (score: 2)
                               ttttatttatatacga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttctttttgacatattttcaacactaattttggcggcatcgtcatgaaagaatccttttatttatatacgaaattacagATCTCAAAAGTTCGAGGATCCTGCCGAAGGTGAAGAAGCTTTGGTCGGCAAATTTAAGAAACTGTATGATGACCTCACCACTGGTTTCCGCAATCTCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA