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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttataattttgcaactcggattctagttttgaacttttggtcacttcattcaaataaaaaacatgatgatgaattgacacatgctcaattttctgaagGCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAAACAGGACTAGCAGATTTGGAGGCTACAAATGACAATGGTCGCCAAAAGC

Basic information

species Zea mays
transcript GRMZM5G863152_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G863152_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g18720.1 (Oryza sativa), 3'ss of exon 14
ccttataattttgcaactcggattctagttttgaacttttggtcacttcattc---aaataaaaaacatgatg----atgaattgacacatgctca-attttctgaagGCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAAACAGGACTAGCAGATTTGGAGGCTACAAATGACAATGGTCGCCAAAAGC
|  || |  |     |||  || | |    |||      |||| ||||||| |   |||||  | |    ||     ||  ||| |||| |  |   ||||||   ||||||||||| ||||||| |  ||||||| |||||||||||| || ||||||||   | | ||  |||||| |||| |||||||  |||||   | |||  
ctgtagagatc----actgagagttttcccttgg----ctggttacttcatactcaaaatagcatatgccatactttatacatttacacctttttttattttcaatagGCAGTTGATGTAATTCTCTCTTGCCGTCAAAAGTTGAATGAGAAAAGTCAAACTCAAGTTGCGAATTTGGCGGCTGCAAATGATGATGGTGCTCCAAAAT
















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|211414958|gb|FL458730.1|FL458730
EST:     TTCTCCGTGGACTGACAAATTCATTACTTGCTGCTAAGAAGCCAGATGAG                         GCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGMAMAGAGTCAA
genomic: TTCTCCGTGGACTGACAAATTCATTACTTGCTGCTAAGAAGCCAGATGAGgtgtgtaagg ... ttttctgaagGCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAA
EST: gi|60359044|gb|DN226017.1|DN226017
EST:     TTCTCCGTGGACTGACAAATTCATTACTTGCTGCTAAGAAGCCAGATGAG                         GCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAA
genomic: TTCTCCGTGGACTGACAAATTCATTACTTGCTGCTAAGAAGCCAGATGAGgtgtgtaagg ... ttttctgaagGCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAA
EST: gi|211309916|gb|FL435262.1|FL435262
EST:     TTCTCCGTGGACTGACAAATTCATTACTTGCTGCTAAGAAGCCAGAT---                         G-AGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAA
genomic: TTCTCCGTGGACTGACAAATTCATTACTTGCTGCTAAGAAGCCAGATGAGgtgtgtaagg ... ttttctgaagGCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAA
EST: gi|71432423|gb|DR813473.1|DR813473
EST:     TTCTCCGTGGACTGACAAATTCATTACTTGCTGCTAAGAAGCCAGATGAG                         GCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAA
genomic: TTCTCCGTGGACTGACAAATTCATTACTTGCTGCTAAGAAGCCAGATGAGgtgtgtaagg ... ttttctgaagGCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcattcaaataaaaaacatgatgatgaattgacacatgctcaattttctgaagGCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAAACAGGACTAGCAGATTTGGAGGCTACAAATGACAATGGTCGCCAAAAGC
                            aattgac  putative branch site (score: 3)
                                             ttttct  putative PPT
     ttcaaataaaaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttataattttgcaactcggattctagttttgaacttttggtcacttcattcaaataaaaaacatgatgatgaattgacacatgctcaattttctgaagGCAGTTGATATAATTCTGTTATGCCGTCGAAAGTTGAATGAAAAGAGTCAAACAGGACTAGCAGATTTGGAGGCTACAAATGACAATGGTCGCCAAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG