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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatattagtccctatgtatccttctgcattgtgccggttcatatttagatttcttgaacacctctctgagcttgcactattggccattattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA

Basic information

species Zea mays
transcript GRMZM2G042552_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042552_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 5
--------------------------gtaatatatta-gtccctatgtatccttctgcat-tgtgccggttcatatttagatttcttgaacacctctctgagcttgcactattggccattattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGT---------GAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA
                           | | || ||      ||| | || ||||   || | |||  |||   |     || |  |||   |     |    |  |   |     |   | |||||||||||||||||| || || || || ||||||| |         ||||| || ||||||||||||||||| |||| |||||||||||| ||||    |||           
gtaatgtccaacgattcaacatatccttcacattttgcaattctagggattcttccatatctctgcgtgtttcaaaaataatgtactgagttctgaaataccttacccggaacttgcgccaatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAACAGATAAGGGAAAGGCTCGCCAAAGTGAGGTCATAAAAGAGTAATGATG---------
















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|78077138|gb|DV505572.1|DV505572
EST:     AAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: AAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|113703876|gb|EE681380.1|EE681380
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGCGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|76293381|gb|DV032949.1|DV032949
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|76931368|gb|DV172713.1|DV172713
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|5740470|gb|AI948160.1|AI948160
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|14255660|gb|BG878568.1|BG878568
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|6095474|gb|AW120141.1|AW120141
EST:     GGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|113675790|gb|DW831183.1|DW831183
EST:     AAAGGTAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: AAAGG-AGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|4646886|gb|AI621961.1|AI621961
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|21759932|gb|BQ635473.1|BQ635473
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTTTACCTGCGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|5929091|gb|AW056383.1|AW056383
EST:     GGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|44901356|gb|CK827901.1|CK827901
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGCGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|149039514|gb|EE046657.2|EE046657
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
EST: gi|14311555|gb|BG901310.1|BG901310
EST:     GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAG                         AGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAGCCTTCAACAAGTGTACCTGAGGAGgtaatatatt ... tattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttagatttcttgaacacctctctgagcttgcactattggccattattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA
                                           attattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatattagtccctatgtatccttctgcattgtgccggttcatatttagatttcttgaacacctctctgagcttgcactattggccattattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGTGAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA