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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatattacaattttcagtgttttataagttgtttctgtgcagtttaaggaaggccttctctgactgacatgggaggcttttctccattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATCAGAATACTTCTATGCCAAGCAACAAGCCGACTATGTAATATCTCAG

Basic information

species Zea mays
transcript GRMZM2G066614_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066614_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g12880.4 (Oryza sativa), 3'ss of exon 4
gtaaatattacaattttcagtgttttataagttgtttctgtgcagtttaaggaaggccttctctgactgacatgggaggcttttctccattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATCAGAATACTTCTATGCCAAGCAACAAGCCGACTATGTAATATCTCAG
    ||||||||  | | | |||| | |  ||| |  || |  |    |   |     |     || |||  | ||||||||  |  ||||||| ||||| || ||||||||||||||||| ||| | ||||| |||||||| ||| ||||| |||||||||||||||||||||| |||||||| ||| | |||
--gtatattacagctct-aatgttctctt-gttatc-ctatataaagaattcataatttctgaggattgagttaggaggcttacc--cattttgcagGCTTTTGTCAGCAGATGAGCTAAAACCTATTATTGGAAATCTCCACCCACCAGAACACTTCTATGCCAAGCAACAAGCTGACTATGTGATAACACAG
















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|32864437|gb|CF004119.1|CF004119
EST:     GATGCACCAGCTAAAAATTCATTTTCACACCTTGATCTGGATAATGATGG                         GCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
genomic: GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGGgtaaatatta ... cattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
EST: gi|5847122|gb|AW000201.1|AW000201
EST:     GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGG                         GCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
genomic: GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGGgtaaatatta ... cattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
EST: gi|211182340|gb|FL049137.1|FL049137
EST:     GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGG                         GCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
genomic: GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGGgtaaatatta ... cattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
EST: gi|6227170|gb|AW155699.1|AW155699
EST:     GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGG                         GCTCTTATCAGCAGATGAGCTAAAGCC
genomic: GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGGgtaaatatta ... cattttgaagGCTCTTATCAGCAGATGAGCTAAAGCC
EST: gi|16816893|gb|BM056087.1|BM056087
EST:     GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGG                         GCTCTTATCAGC
genomic: GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGGgtaaatatta ... cattttgaagGCTCTTATCAGC
EST: gi|5343190|gb|AI795375.1|AI795375
EST:     GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGG                         GCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
genomic: GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGGgtaaatatta ... cattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
EST: gi|32864436|gb|CF004118.1|CF004118
EST:     GATGCACCAGCTAAAAATTCATTTTCACACCTTGATCTGGATAATGATGG                         GCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
genomic: GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGGgtaaatatta ... cattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATC
EST: gi|6095356|gb|AW120023.1|AW120023
EST:     GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGG                         GCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCC
genomic: GATGCACCAGCTAAAAAGTCATTTTCACACCTTGATCTGGATAATGATGGgtaaatatta ... cattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttaaggaaggccttctctgactgacatgggaggcttttctccattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATCAGAATACTTCTATGCCAAGCAACAAGCCGACTATGTAATATCTCAG
                      gactgac  putative branch site (score: 2)
                                     cttttctccatttt  putative PPT
                                              attttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatattacaattttcagtgttttataagttgtttctgtgcagtttaaggaaggccttctctgactgacatgggaggcttttctccattttgaagGCTCTTATCAGCAGATGAGCTAAAGCCTGTAATTGGTAATCTCCATCCATCAGAATACTTCTATGCCAAGCAACAAGCCGACTATGTAATATCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA