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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatggaagtatagggtggtcggctgcatttaatttattatccaagaagattaagtaaaaaggaattggcttctcattgaatttccctatcactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTCGAATCAGTTTTCGAGCCATTAGGGGCCGAGGCTGAGTTGAGTGTGTGAA

Basic information

species Zea mays
transcript GRMZM2G047564_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047564_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g39344.3 (Oryza sativa), 3'ss of exon 8
ttatggaagtatagggtggtcggctgcatttaatttattatccaagaagattaagtaaaaagg---aattggcttctcattgaatttccctatcactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTCGAATCAGTTTTCGAGCCATTAGGGGCCGAGGCTGAGTTGAGTGTGTGAA
   |   ||   || |   |    |  | | || ||  |    | |||   ||   | | |     | |   | | |   | ||||||| | ||| |||| ||||||| |||||||| ||||| ||||||||||| ||  ||| ||  ||||| ||||||||||| || |||||||  || ||||||||||| | ||| ||| 
---taagagaggagagaaataatatttactaaacttggtggagatgaactctatagatatatatttactaaacgtatagctaaatttccttttcaatttgtagAATCCAAAGTGGAAGCCAGCAACTCTGGAAGACGTGGACAAGGGTGAGGTGGAATCAGTTTTTGAACCATTAGCTGCTGAGGCTGAGTTAAATGTATGAT
















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|37379970|gb|CF626760.1|CF626760
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|76012489|gb|DT939659.1|DT939659
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|91873503|gb|EB403460.1|EB403460
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCCCTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|18166670|gb|BM336509.1|BM336509
EST:     AACGATTATTGTATGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTATGGAAGAAGTAAACATGGCCGAGGTC
genomic: AACGATT-TTGT-TGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|71331740|gb|DR802726.1|DR802726
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|78078184|gb|DV506599.1|DV506599
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|113701450|gb|EE678954.1|EE678954
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|88750160|gb|DY534301.1|DY534301
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|60345004|gb|DN211977.1|DN211977
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|149097994|gb|EE183939.2|EE183939
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|211171388|gb|FL176740.1|FL176740
EST:     NAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAR                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|166504034|gb|EG317726.1|EG317726
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCAC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCAC
EST: gi|76012490|gb|DT939660.1|DT939660
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|18165516|gb|BM335355.1|BM335355
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|60399515|gb|DN232327.1|DN232327
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|211528664|gb|FL445658.1|FL445658
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTG
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|211171385|gb|FL176737.1|FL176737
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|211171387|gb|FL176739.1|FL176739
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
EST: gi|88749306|gb|DY533447.1|DY533447
EST:     GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAG                         AATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC
genomic: GAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACCAGgcaagttatc ... cactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagattaagtaaaaaggaattggcttctcattgaatttccctatcactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTCGAATCAGTTTTCGAGCCATTAGGGGCCGAGGCTGAGTTGAGTGTGTGAA
                                    tttccctatcacttt  CT-rich tract
     ttaagtaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatggaagtatagggtggtcggctgcatttaatttattatccaagaagattaagtaaaaaggaattggcttctcattgaatttccctatcactttgcagAATCCGAAGTGGAATCCAGCCACTCTGGAAGAAGTAAACATGGCCGAGGTCGAATCAGTTTTCGAGCCATTAGGGGCCGAGGCTGAGTTGAGTGTGTGAA

- - - - - - - - - - cggctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - aagtaaaa