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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctagcaatagggtagaagttccctctgcccctattatttcactttttctaatcttgggatgcaaggagaatactgaacaagtcattttgtattttcagAAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTAACAACCCCGCCTCCCCGTCTTGCTGATTTGTATGTTACTGCTGACACATT

Basic information

species Zea mays
transcript GRMZM2G107629_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107629_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 5
agctagcaatagggtagaagttccctctgcccctattatttcactttttctaatcttgggatgcaaggagaatactgaacaagtcattttgta-ttttcagAAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTAACAACCCCGCCTCCCCGTCTTGCTGATTTGTATGTTACTGCTGACACATT
 | |     |     |    |           |||  |     |        || || ||    ||| | ||||   || |  |  |||| |  || ||||||||||||| ||||||||||| ||| || ||||| |||||||||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||
tgttctttctttatcatggttaataaacagggctaacagcaagccacaaaatattttaggtca-aagcaaaataaccaagatttttttttttggttctcagAAATGCACAAAGATGGGGGAACTGGACTGGCTCCTTGGCCTGCTCGATTAACAACTCCACCTCCCCGTCTTGCTGATTTGTATGTCACTGCTGACACATT
















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|26559775|gb|CA832010.1|CA832010
EST:     TTCAGTATGGGGAGTGCCAATGGAAGCTTGCATTACTCCGTATCCTGAAC                         AAATTGGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATT
genomic: TTCAGTATGGGGAGTGCCAATGGAAGCTTGCATTACTCCGTATCCTGAACgtgagtagtt ... gtattttcagAAA-T-GCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATT
EST: gi|87157567|gb|DY402356.1|DY402356
EST:     TTCAGTATGGGGAGTGCCAATGGAAGCTTGCATTACTCCGTATCCTGAAC                         AAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTAA
genomic: TTCAGTATGGGGAGTGCCAATGGAAGCTTGCATTACTCCGTATCCTGAACgtgagtagtt ... gtattttcagAAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTAA
EST: gi|32825265|gb|CD964987.1|CD964987
EST:     TTCAGTATGGGGAGTGCCAATGGAAGCTTGCATTACTCCGTATCCTGAAC                         AAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTA
genomic: TTCAGTATGGGGAGTGCCAATGGAAGCTTGCATTACTCCGTATCCTGAACgtgagtagtt ... gtattttcagAAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTA
EST: gi|22935914|gb|BU572189.1|BU572189
EST:     TTCAGTATGGGGAGTGCCAATGGAAGCTTGCATTACTCCGTATCCTGAAC                         AAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTAA
genomic: TTCAGTATGGGGAGTGCCAATGGAAGCTTGCATTACTCCGTATCCTGAACgtgagtagtt ... gtattttcagAAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctaatcttgggatgcaaggagaatactgaacaagtcattttgtattttcagAAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTAACAACCCCGCCTCCCCGTCTTGCTGATTTGTATGTTACTGCTGACACATT
  ttctaat  putative branch site (score: 2)
                                              tattttc  putative PPT
                                      tcattttgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctagcaatagggtagaagttccctctgcccctattatttcactttttctaatcttgggatgcaaggagaatactgaacaagtcattttgtattttcagAAATGCACAGAGATGGGGGAAGTGGGCTAGCTCCCTGGCCTGCTCGATTAACAACCCCGCCTCCCCGTCTTGCTGATTTGTATGTTACTGCTGACACATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT