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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatctgcctcttgcttggttcatttgtcacttctggagcccttggagttccaatttttttttctttttaatttcaattgacttgatcctcttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCGAAAGGTTCCTCAA

Basic information

species Zea mays
transcript GRMZM2G060870_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060870_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g40890.1 (Oryza sativa), 3'ss of exon 3
---------tgatctgcctcttgcttggttcatttgtcacttctggagcccttggagttccaatttttttttctttttaatttcaattgacttgatcctcttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCGAAAGGTTCCTCAA
         |||| ||| |  |     ||     | || ||| ||||||||   || ||| | ||| |||| ||    ||   ||| |||  | || |  |  |  |||||||||||||| || ||||||||||| |||||||| ||||  ||  |||||||||||||||||||||| |||||||||||||| || |||||||| ||||
actttagaatgatttgcttacttagaagtgtccatatcccttttggagcccacagatttctagtttgttttgct----aa---caactgatctaattcattctt--cagAGGCTGGAAAATAAATATTCTTCAGACCCATCAAAATATGAGCAATTGTACAGCATGGTTCAGGAAGAGGTTCAAAACAAGACTGCAAAAGGTTCGTCAA
















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|45567822|gb|CK985763.1|CK985763
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCGAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|60346084|gb|DN213057.1|DN213057
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|17932440|gb|BM269400.1|BM269400
EST:     AGCGGCAATATCACA                         AGGCTGGAAAACAAG-ATTCTTCAGATCCATCAAAGTATGGACACATGTAC
genomic: AGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|60401114|gb|DN233921.1|DN233921
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|211107785|gb|FL216765.1|FL216765
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCGAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|6223799|gb|AW154930.1|AW154930
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|5686769|gb|AI939862.1|AI939862
EST:     GCGGCAATATCNCA                         AGGCTGGAAANCAAGTATTTTTCAGATCCATCAAAGTATGGACNCTTGTAC
genomic: GCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|22542222|gb|BU092660.1|BU092660
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|60401080|gb|DN233887.1|DN233887
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|31359252|gb|CD443609.1|CD443609
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|6223801|gb|AW154932.1|AW154932
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         TGGTTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|71770686|gb|DR968623.1|DR968623
EST:     CAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
genomic: CAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|26559123|gb|CA831358.1|CA831358
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|211107786|gb|FL216766.1|FL216766
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|60399775|gb|DN232585.1|DN232585
EST:     CAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
genomic: CAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|6223798|gb|AW154929.1|AW154929
EST:     TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACTTGTAC
genomic: TTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|211296159|gb|FL473353.1|FL473353
EST:     TGGAGCTGGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCGAAGTATGGACACTTGTAC
genomic: TGGAGCT-GCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC
EST: gi|211365280|gb|FL463922.1|FL463922
EST:     GATATCAGCGGCAATTTCACA                         AGGCTGGAAAACAAGTATTCTTCAGATCCATCGAAGTATGGACACTTGTAC
genomic: GATATCAGCGGCAATATCACAgtaagcaaat ... cttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttccaatttttttttctttttaatttcaattgacttgatcctcttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCGAAAGGTTCCTCAA
                                    cttgatcctcttct  CT-rich tract
       aatttttttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatctgcctcttgcttggttcatttgtcacttctggagcccttggagttccaatttttttttctttttaatttcaattgacttgatcctcttctgtcagAGGCTGGAAAACAAGTATTCTTCAGATCCATCAAAGTATGGACACATGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCGAAAGGTTCCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT