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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGTTGTCCTTACTAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgaccttttcctgttctctttgttcactcgattttactgctcaggtgaaaatctgaaagtctgcttttatcaacctaatttttag

Basic information

species Zea mays
transcript GRMZM2G095252_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 8
AAAGGTTGTCCTTACTAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgaccttttcctgttctctttg--ttcactcgattttactgctcaggtgaaaatct-----gaaagtctgctttta---tcaacctaatttttag
|||||| |||||||  |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||||||||||| || ||||||||||| ||||| | | |  | |   |    |  ||   ||  | | ||  | |  | ||  |     | |       ||   || || ||   || |||   | |||| 
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatggttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
AAAGGTTGTCCTTACTAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgaccttttcctgttctctttgttcactcgattttactgctcaggtgaaaatctgaaagtctgcttttatcaacctaatttttag-------------
 ||||| || || || || ||  | || ||||||||||||||||| || |||||||| | ||| |  ||||| |||||||||||||  || || |||||||||| |  || | ||    | | | | | ||||  | | |  ||| || |  ||  |   |  | | | ||| || ||  || ||   ||             
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtcttt--ccatctctctctttttctctccactgaaatgt-ttgcacatgcaaacgtggcatgggcaggtttcatgaagatatttcacagaaaacatgactga

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 8
AAAGGTTGTCCTTACTAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgaccttttcctgttctctttgttcactc---gattttac-tgctcaggtgaaaatctgaaagtctgcttttatcaacctaatt-tttag
|||||| || ||||| || ||  | || || |||||||| ||||| ||||||||||| | ||| | |||| | |||||||| |||| ||| ||||||||||| |||  |  |   ||       |    ||| |   || |  |  ||     |   || | ||    |||  | |||   |  |  |  || ||
AAAGGTGGTGCTTACCAAGGATACAACCACCATTGTTGGAGATGGGAGCACCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatctgtcctctcactcactcacacacacagagagtaaatatgtgtttgctgaactttgttgatct-ttcttacatatgtgttgattcag

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|32837509|gb|CD977187.1|CD977187
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|32932965|gb|CF037777.1|CF037777
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|33092673|gb|CF052667.1|CF052667
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGGGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|32934171|gb|CF038983.1|CF038983
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAACCTCATTGAG                         GCAGCAGACCAAGAATATGAAAAGGAAAAGCTCAATGAGCGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|211046936|gb|FL343169.1|FL343169
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|498197|gb|T20345.1|T20345
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAA
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAA
EST: gi|32935108|gb|CF039920.1|CF039920
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|32931097|gb|CF035909.1|CF035909
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|32836365|gb|CD976043.1|CD976043
EST:     CGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|32935122|gb|CF039934.1|CF039934
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|32838764|gb|CD978445.1|CD978445
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|211173892|gb|FL341459.1|FL341459
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAVATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|32930569|gb|CF035381.1|CF035381
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
EST: gi|33097092|gb|CF057052.1|CF057052
EST:     CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAG                         GCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG
genomic: CCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgacc ... taatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGTTGTCCTTACTAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgaccttttcctgttctctttgttcactcgattttactgctcaggtgaaaatctgaaagtctgcttttatcaacctaatttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG