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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttcatcagatgtttcttgtccagcatattattcttctttttaggcagactgagtactcttagcatatttgctgtgattgtgctatttgaaagagataatgtcatgatacttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAGGCTGCATGAACAAGTGGAG

Basic information

species Zea mays
transcript GRMZM2G064197_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064197_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g12750.2 (Oryza sativa), 3'ss of exon 3
gtatggttcatcagatgtttcttgtccagcatattattcttctttttaggcagactgagtactcttagcatatttgctgtgattgtgctatttgaaagagat----aatgtcatg-atacttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAGGCTGCATGAACAAGTGGAG
||| | | |||  |||  |  |  |  | ||| |  |||| | || | |  |    || || | | |  ||| |    ||| |||||||| || ||| |||     |||||||    |||||| | |||||  ||||| || || |||||| || |||| ||||||||| |||||||||| ||||||||||||||||||
gtaagctccatgggatactcatcctgga-catttgtttctccattctggcaaatacgaatattttaataatagtgctcgtg-ttgtgctagtttaaaaagagttaaaatgtcacatgtacttgttacagAAATCAAGAGGTCAAGGAAGCATTGCGAGCTCAGATGGAAATGCAACGAAGACTGCATGAACAAGTGGAG
















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|91051798|gb|EB162216.1|EB162216
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAACACTGAGAGCGCAGATGGAGGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|74233858|gb|DT641772.1|DT641772
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|22473367|gb|BU037847.1|BU037847
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCTCTGAGAGCGCAGATGGA
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGA
EST: gi|74232734|gb|DT640648.1|DT640648
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|74232735|gb|DT640649.1|DT640649
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|26558692|gb|CA830927.1|CA830927
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCTCTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|76292002|gb|DV031570.1|DV031570
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|76918384|gb|DV167269.1|DV167269
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|87156993|gb|DY401782.1|DY401782
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCTCTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|76292621|gb|DV032189.1|DV032189
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|50333124|gb|CO528250.1|CO528250
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|78076222|gb|DV504656.1|DV504656
EST:     GTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: GTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|74233857|gb|DT641771.1|DT641771
EST:     TGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
genomic: TGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|88755721|gb|DY539862.1|DY539862
EST:     CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAA
genomic: CAAAGTGGAATGAGTGTGTCCCCTAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAG
EST: gi|71436515|gb|DR817565.1|DR817565
EST:     AGAGTGGAATGAGTGTGTCCCCCTAGAGTTGCTGCCCAGGATATGAAAGA                         AAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAAGTGCA-CGAA
genomic: AAAGTGGAATGAGTGTGTCCCC-TAGAGTTGCTGCCCAGGATATGAAAGAgtatggttca ... cttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAA-GTGCAACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttgctgtgattgtgctatttgaaagagataatgtcatgatacttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAGGCTGCATGAACAAGTGGAG
                   tatttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttcatcagatgtttcttgtccagcatattattcttctttttaggcagactgagtactcttagcatatttgctgtgattgtgctatttgaaagagataatgtcatgatacttgctgcagAAGCCAAGAAGTTAAAGAAGCACTGAGAGCGCAGATGGAAGTGCAACGAAGGCTGCATGAACAAGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG