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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGAACTCAAAATGCTGAGAAAGAGTTTAAATTTCAAGGCAACACCAATGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcccccatacttttggctaagtttcttcttcctgtttttcctccattaaattgttggctgcagatattctatatataaatcacaaagtatctc...

Basic information

species Zea mays
transcript GRMZM2G056166_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056166_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g40450.3 (Oryza sativa), 5'ss of exon 7
AGCTGAACTCAAAATGCTGAGAAAGAGTTTAAATTTCAAGGCAACACCAATGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcccccatacttttggctaagtttcttcttcctgtttttcctccattaaattgttggctgcagatattctatatataaatcacaaagtatctc-
|||||||||||||| ||| || |||||||| ||||| | |||||  |||||||||||||||||||||||||||||||| ||||||||||||||||| |||||| || || | | |    |   | | ||             |||      ||  |    ||  || | |||   |  ||      |    |    |||  
AGCTGAACTCAAAAAGCTAAGGAAGAGTTTGAATTTTAGGGCAAATCCAATGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAAAAGgtaattctctcgcttgagatatac-atgtaaggaaaggaaaatttaagattatagaccatttacctactgattcacagtaggacctttggcagtcttcttt
















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|148948865|gb|EC894276.2|EC894276
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|148999955|gb|EE037020.2|EE037020
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|113700974|gb|EE678478.1|EE678478
EST:     TGCCCAGTTTTTATAAAGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATACTTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|18165854|gb|BM335693.1|BM335693
EST:     CCCAAGGTTGAGTTGAAGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: CCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|149096093|gb|EE181777.2|EE181777
EST:     CCAGCTTTTATAAGGACCCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: CCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|78021209|gb|DV489596.1|DV489596
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|148972775|gb|EE023749.2|EE023749
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTGGAGGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|60401089|gb|DN233896.1|DN233896
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTCGAAGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|149096714|gb|EE182487.2|EE182487
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|211309531|gb|FL415789.1|FL415789
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcc ... ttgatcttagATACCTACAACAAGAGCTAGGTCACCAAAGCTTGGTCGCTCCAAGAACACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGAACTCAAAATGCTGAGAAAGAGTTTAAATTTCAAGGCAACACCAATGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAGgtacttgtcccccatacttttggctaagtttcttcttcctgtttttcctccattaaattgttggctgcagatattctatatataaatcacaaagtatctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccatac