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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattatgtatgtcttattttctttaactggacatacaaaatcgtttacacaattcttgtttgatgactactagtgatcagtctctgttttcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG

Basic information

species Zea mays
transcript GRMZM5G896731_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G896731_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g51800.1 (Oryza sativa), 3'ss of exon 2
tgattatgtatgtcttattttctttaactggacatacaaaatcgtttacacaat------tcttgtttgatgactactagtgatcagtctctgttt-tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
       |  |||   | || ||||||||||||||| ||||  | ||| || ||       ||  | ||||||||  | ||||| ||||| | ||   |  |||||||| || ||||||||||||||||||||||| ||||||||||||||||| |||
-------gcttgtagaaattcctttaactggacataaaaaaatggttataccatactgaccctgatctgatgactcttggtgataagtcttttttggcctattgcagGTTGGGCCACTTGCTGCCTATTATAAACTACCACTTAATCGTGTCCTTGTG

upper sequence: GRMZM5G896731_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g22610.1 (Oryza sativa), 3'ss of exon 4
tgattatgtatgtcttattttctttaactggacatacaaaatcgtttaca------caattcttgtttgatgactactagtgatcagtctctgttt--tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
          |||   | |||||||||||||| ||| ||||  | ||| |        |  ||  | ||||||||| | ||||| |||| || |||   |  |||||||| || ||||||||||||||||||||| | ||||||||||| ||||| |||
--------cttgtagaaatttctttaactggaaataaaaaaatggttataatacactgagcctgatctgatgactattggtgataagtccctttttggcctattgcagGTTGGGCCACTTGCTGCCTATTATAAATTACCACTTAATCGCGTCCTTGTG
















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|89248113|gb|DY619899.1|DY619899
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|78109136|gb|DV527553.1|DV527553
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|88756830|gb|DY540971.1|DY540971
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|71438321|gb|DR819371.1|DR819371
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|76293027|gb|DV032595.1|DV032595
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGTCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|89250808|gb|DY622594.1|DY622594
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|91053266|gb|EB163684.1|EB163684
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACT
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACT
EST: gi|78109135|gb|DV527552.1|DV527552
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|60358732|gb|DN225705.1|DN225705
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|91050003|gb|EB160421.1|EB160421
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
EST: gi|78085320|gb|DV513713.1|DV513713
EST:     CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCT                         GTCGGCCCCACT-GCTGCCTATTATAAACTGCCACTTAATC
genomic: CTGTTCTTCTTGCCAAGCCCCAGACTTATATGAATCTCAGTGGAGAATCTgtaagtgaca ... tcacttgcagGTCGGCCC-ACTTGCTGCCTATTATAAACTGCCACTTAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacacaattcttgtttgatgactactagtgatcagtctctgttttcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG
             gtttgat  putative branch site (score: 5)
                                    tctctgttttcactt  putative PPT
      aattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattatgtatgtcttattttctttaactggacatacaaaatcgtttacacaattcttgtttgatgactactagtgatcagtctctgttttcacttgcagGTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC