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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acccatgagcgtttcaacgtttcgtcgttttaataaccatggaaatgattgctgtgtgtttatgggtttacactctcttttgactggttttattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTGGAGGTTTATAACTACGCCCTTGATCAAAACAAATCTGAAGAGAAG

Basic information

species Zea mays
transcript GRMZM2G056393_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 5
acccatgagcgtttcaacgttt-cgtcgttttaataaccatggaaatgattgctgtgtgtttatgggtttacactctcttttgactggttttattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTGGAGGTTTATAACTACGCCCTTGATCAAAACAAATCTGAAGAGAAG
   |||| |  |   ||   |  |  |  |   ||   | |  || |  ||||||  |||||  |  ||| ||    |||       |  |  |||   ||||||| || || ||||||||||| ||||| || ||| |||| || ||  |||| ||| | | |||||| ||||||||||||||||| |||||||||
-atcatgggaatgggaaaactaacaactgtgagattttctttaaattagttgctggatgtttcagaatttgcatgagcttacattctgactggtttcgcagGGTGTCCAGCCGCTTCTTGATGGTGTGCTTGACTATTTACCTTGTCCAATGGAAGTTGAAAGCTACGCACTTGATCAAAACAAATCAGAAGAGAAG
















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|22491486|gb|BU051409.1|BU051409
EST:     TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAG                         GGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
genomic: TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAGgttcgtggct ... tattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
EST: gi|67019503|gb|CO448252.1|CO448252
EST:     TGGCACGGAGGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAG                         GGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
genomic: TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAGgttcgtggct ... tattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
EST: gi|19436218|gb|BM952628.1|BM952628
EST:     TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAG                         GGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACC
genomic: TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAGgttcgtggct ... tattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACC
EST: gi|19351127|gb|BM895659.1|BM895659
EST:     TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAG                         GGTGTTCAACCA
genomic: TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAGgttcgtggct ... tattttatagGGTGTTCAACCA
EST: gi|32931849|gb|CF036661.1|CF036661
EST:     TGGCACAGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAG                         GGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
genomic: TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAGgttcgtggct ... tattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
EST: gi|87154041|gb|DY398830.1|DY398830
EST:     TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAG                         GGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
genomic: TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAGgttcgtggct ... tattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
EST: gi|118406757|gb|EH038205.1|EH038205
EST:     TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAG                         GGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG
genomic: TGGCACGGAAGTTCATACCAGTATACATGGGAAGTGCATTCAAAAATAAGgttcgtggct ... tattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgctgtgtgtttatgggtttacactctcttttgactggttttattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTGGAGGTTTATAACTACGCCCTTGATCAAAACAAATCTGAAGAGAAG
                                ttttgac  putative branch site (score: 3)
                                          ttttatttt  putative PPT
                                       tggttttattttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acccatgagcgtttcaacgtttcgtcgttttaataaccatggaaatgattgctgtgtgtttatgggtttacactctcttttgactggttttattttatagGGTGTTCAACCACTTCTTGATGGCGTGCTGGATTATCTACCGTGCCCGTTGGAGGTTTATAACTACGCCCTTGATCAAAACAAATCTGAAGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA