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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattagaattgtgaccacacatagagtaggaaggtttcattatgttactagatttggtgcacattgtacataatgctgatcaatatctcctttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGCTTTCTTGCCAGAAGTACAGAGTGCTGATAGGAAAATACCATTCAGAGAG

Basic information

species Zea mays
transcript GRMZM2G307252_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G307252_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 1
------------------cattagaattgt-gaccaca-catagagtaggaaggtttcattatgttactagatttggtgcacattgtaca--taatgctgatcaa---tatctcctttaatatagA-GAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGCTTTCTTGCCAGAAGTACAGAGTGCTGATAGGAAAATACCATTCAGAGAG
                    || |||| |  ||   || |||  | ||    | | |   |   ||| |   ||  ||      || |    |  ||| | |      | | |  ||||   || |  ||||||  || || ||| | || || |||||||| |||||||||||  ||||| |||||||||| |||||||                          
agatatttgggtgtttgctctttgaatggaagattgcatcatctattatattgctattgattacttatttatttctgtttttggtgaatggctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTGCTTCATCTTGTCAGGCCATTTCTTTCTTTCCTGCCAGAAGTTCAGAGTG--------------------------
















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|211360868|gb|FL288052.1|FL288052
EST:     GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
EST: gi|211517031|gb|FL210552.1|FL210552
EST:     GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
EST: gi|211360869|gb|FL288053.1|FL288053
EST:     GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
EST: gi|211517030|gb|FL210551.1|FL210551
EST:     GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
EST: gi|211360870|gb|FL288054.1|FL288054
EST:     GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
EST: gi|211360872|gb|FL288056.1|FL288056
EST:     GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
EST: gi|211360871|gb|FL288055.1|FL288055
EST:     GGTGCTCAGGTCTGCCACTTGRCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
EST: gi|211204810|gb|FL296834.1|FL296834
EST:     GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGTC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
EST: gi|211360873|gb|FL288057.1|FL288057
EST:     GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAG                         AGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC
genomic: GGTGCTCAGGTCTGCCACTTGGCACTTCGCCGGCGACGAGCACCTAACAGgtacgcccag ... tttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactagatttggtgcacattgtacataatgctgatcaatatctcctttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGCTTTCTTGCCAGAAGTACAGAGTGCTGATAGGAAAATACCATTCAGAGAG
                                      tatctccttt  CT-rich tract
                                             tttaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattagaattgtgaccacacatagagtaggaaggtttcattatgttactagatttggtgcacattgtacataatgctgatcaatatctcctttaatatagAGAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGCTTTCTTGCCAGAAGTACAGAGTGCTGATAGGAAAATACCATTCAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT