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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttagttagttcctgctcgatgggtggtcagattacgggttacataattacatgcttgcttcgattgctttctcgtgctaatgtggctcctgctgcacagGTATGGCTTCGACATTCGGTGCCACTTCTACTGTCGGCCTTATGGCTGCTCCAACAGGGAAGAATGTGCGCCTTCAGAGGAGGGTGAACTTCAGAGTAAG

Basic information

species Zea mays
transcript GRMZM2G133698_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 1
---gttagttagttcctgctcgatgggtggtcagattacgggttacataattacatgcttgctt-cgattgctttctcgtgctaatgtggctcctgctgcacagG----TATGGCTTCGACATTCGGTGCCACTTCTACTGTCGGCCTTATGGCTGCTCCAACAGGGAAGAATGTGCGCCTTCAGAGGAGGGTGAACTTCAGAGTAAG
    | |  | |  ||| | |    | |  ||   || | |  || |   |||   || |||||  ||||| |    | || |||||| |    ||||| |||||     |||||||| |||||||||||||||||||| || ||||| |||||||| ||||| || |    |||   |   ||        |   ||  |   |  |
actttcatgtgggacctccacctcagct--tccattttctgaatagaagcttaa--gcatgcttatgattgttgctccatgttaatgttgtcattgctgaacagGAAATCATGGCTTCAACATTCGGTGCCACTTCTACGGTTGGCCTCATGGCTGCGCCAACCGGAAT---TGTAT-CAGACAAGAAGCCATCTTCTCTATCTTCGG
















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|211501121|gb|FL128998.1|FL128998
EST:     TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGCGNTAAG                     
genomic: TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGC-----Ggtaaggtgag ... tgctgc
EST: gi|211505822|gb|FL129027.1|FL129027
EST:     TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGCGGTAAG                     
genomic: TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGC-----Ggtaaggtgag ... tgctgc
EST: gi|211312615|gb|FL128951.1|FL128951
EST:     TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGCGGTAAG                     
genomic: TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGC-----Ggtaaggtgag ... tgctgc
EST: gi|211316666|gb|FL128979.1|FL128979
EST:     TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGCG                         GTATGGCTTCGACATTCGGTGCCACTTCTACTGTCGGCCTTATGGCTGCTC
genomic: TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGCGgtaaggtgag ... tgctgcacagGTATGGCTTCGACATTCGGTGCCACTTCTACTGTCGGCCTTATGGCTGCTC
EST: gi|211314638|gb|FL128959.1|FL128959
EST:     TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGCGGTAAG                     
genomic: TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGC-----Ggtaaggtgag ... tgctgc
EST: gi|18659978|gb|BM500622.1|BM500622
EST:     TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGCGGTAAG                     
genomic: TCCGCCAGCCTTATCCTCCTCCCCGTCTCCGGCTCCAACCCGCAAGCGC-----Ggtaaggtgag ... tgctgc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacatgcttgcttcgattgctttctcgtgctaatgtggctcctgctgcacagGTATGGCTTCGACATTCGGTGCCACTTCTACTGTCGGCCTTATGGCTGCTCCAACAGGGAAGAATGTGCGCCTTCAGAGGAGGGTGAACTTCAGAGTAAG
                              tgctaat  putative branch site (score: 2)
                                         ctcctgct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttagttcctgctcgatgggtggtcagattacgggttacataattacatgcttgcttcgattgctttctcgtgctaatgtggctcctgctgcacagGTATGGCTTCGACATTCGGTGCCACTTCTACTGTCGGCCTTATGGCTGCTCCAACAGGGAAGAATGTGCGCCTTCAGAGGAGGGTGAACTTCAGAGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG