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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaagaatacctttgtttatccttttctgctgtagacgcactcgtgactcttagtgtttggcatgatgtcctgcttaacacaatgctaaaattgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGCTACGATGGAAGATTTCTATGATGTAAAACTAACTGAAATTGATGGACAA

Basic information

species Zea mays
transcript GRMZM2G073788_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073788_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g15594.1 (Oryza sativa), 3'ss of exon 1
acaagaatacctttgtttatccttttctgctgtagacgcactcgtgactcttagtgtttggcatgatgtcctgcttaacacaatgct----aaaattgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGCTACGATGGAAGATTTCTATGATGTAAAACTAACTGAAATTGATGGACAA
    |  ||  |||   | || ||    |    |  |   ||| |    || | | |||| |||| |  | || |||||  ||||      ||| |||||||||||||||||| |||||||  |||||||| |||||||||||||| |||||||| || ||||| |||||||||||||||||  |||||||||| |||||||| 
----gtttaaatttccatctctttacaagaatcattcattctctttggactcattatttgacatgctaccttggttaacgtaatgtccgaaaaatttgtgacagAGAAGATGGTAAACTGAAATGTGGATATTCAAGTTTTAGAGGGAAGAGAGCCACCATGGAGGATTTCTATGATGTAAAGTTAACTGAAATCGATGGACAG
















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|78125863|gb|DV544247.1|DV544247
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
EST: gi|71438954|gb|DR820004.1|DR820004
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
EST: gi|149077211|gb|EE165878.2|EE165878
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
EST: gi|50330958|gb|CO526084.1|CO526084
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
EST: gi|149080584|gb|EE169627.2|EE169627
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
EST: gi|149078330|gb|EE167097.2|EE167097
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
EST: gi|50326055|gb|CO521181.1|CO521181
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
EST: gi|91878953|gb|EB408910.1|EB408910
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCCAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
EST: gi|91051229|gb|EB161647.1|EB161647
EST:     GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAG                         AGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC
genomic: GCCGTGCCCCTGGCGCACGACGGCGGCTACGCCAGCGGCGGATGGGAGAGgtaatgtatg ... attgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactcttagtgtttggcatgatgtcctgcttaacacaatgctaaaattgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGCTACGATGGAAGATTTCTATGATGTAAAACTAACTGAAATTGATGGACAA
                                      tgctaaa  putative branch site (score: 2)
                                         taaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaagaatacctttgtttatccttttctgctgtagacgcactcgtgactcttagtgtttggcatgatgtcctgcttaacacaatgctaaaattgtgacagAGAAGATGGCAAACTGAGTTGTGGATACTCAAGTTTTAGAGGCAAGAGAGCTACGATGGAAGATTTCTATGATGTAAAACTAACTGAAATTGATGGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA