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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagatgacacccttgtacaacagccggtttttttatttgacgttttttagtataaagttgtactgttgagagtcaaataaaaagaaatggaggtagtattatttatttcaagtcaatgcttatcaaacactggtggctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAGTATCACGCAGACTGCATCAAGAAATGGCTGCAGGTGAAGAACGCTTGCC

Basic information

species Zea mays
transcript GRMZM2G118344_T05
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118344_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g07070.8 (Oryza sativa), 3'ss of exon 7
gtaagaagatgacacccttgtacaacagccggtttttttatttgacgttttttagtataaagttgtactgttgagagtcaaataaaaagaaatggaggtagtattatttatttcaagtcaatgcttatcaaacactggtggctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAGTATCACGCAGACTGCATCAAGAAATGGCTGCAGGTGAAGAACGCTTGCC
                                              ||    ||||  |  ||   | | |    | |   |||   |     | ||    | |||   | | ||||| | |  | ||| |  ||   |   |  ||||||||||| |||||    |||||| |  | |||| ||| ||||||   |||  || ||||    | ||||||||||| |||||||||||||||||| | ||||
----------------------------------------------gtaagatagtggatggtaccaatctacctactatgatagcgattcccgcagcgcattttacgcaatacaagttact--taatccacaacctctttttcactgcagGAGGAATACAAGCATGAGGACACACTTGGGAGGCTGAAATGCGGCCACGGGTTTCACTGCAATTGCATCAAGAAGTGGCTGCAGGTGAAGAACACCTGCC
















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|74242191|gb|DT650105.1|DT650105
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|4646562|gb|AI491300.2|AI491300
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCCCAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|9461925|gb|BE453973.1|BE453973
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|12046750|gb|BF728889.1|BF728889
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACCCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|91871238|gb|EB401314.1|EB401314
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|50334693|gb|CO529819.1|CO529819
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|6563804|gb|AW231336.1|AW231336
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|60347420|gb|DN214393.1|DN214393
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACCCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|14245256|gb|BG873838.1|BG873838
EST:     TGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: TGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|67019275|gb|CO448024.1|CO448024
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|88748917|gb|DY533058.1|DY533058
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|67016991|gb|CO445740.1|CO445740
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|116823896|gb|EC867473.1|EC867473
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|71427069|gb|DR808119.1|DR808119
EST:     CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
genomic: CTGCCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAG
EST: gi|166483900|gb|EG135194.1|EG135194
EST:     CCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTG                         GAGGATTACAAATTCGAGGACTCT
genomic: CCCGTACTCATGATGATAATGAGAGCGCAAGATGTGTAATTTGCCTGgtaagaagat ... ctggctgcagGAGGATTACAAATTCGAGGACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtagtattatttatttcaagtcaatgcttatcaaacactggtggctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAGTATCACGCAGACTGCATCAAGAAATGGCTGCAGGTGAAGAACGCTTGCC
     tattatttatttcaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaagatgacacccttgtacaacagccggtttttttatttgacgttttttagtataaagttgtactgttgagagtcaaataaaaagaaatggaggtagtattatttatttcaagtcaatgcttatcaaacactggtggctggctgcagGAGGATTACAAATTCGAGGACTCTGTCGGGAAGCTAAAATGCAATCACAAGTATCACGCAGACTGCATCAAGAAATGGCTGCAGGTGAAGAACGCTTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC