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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattttttcctgttcatctccaatccttggtttgctacttttgtgattctgttctttccaaattgacaaatttgtatggttttatctgtttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAATTATGAAGGACAAGCATACTAAGATGCCTCGTGGATTTGGATTTGTTAC

Basic information

species Zea mays
transcript GRMZM2G139643_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139643_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g12850.1 (Oryza sativa), 3'ss of exon 3
-----atattttttcctgttcatctccaatccttggtttgctacttttgtgattctgttctttccaaattgacaaatttgtatggttttatctgtttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAATTATGAAGGACAAGCATACTAAGATGCCTCGTGGATTTGGATTTGTTAC
     ||| | | |  | | | |  |||||  |   | |  | ||    | ||||   | ||||| | ||||||||  |||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
cttcaatactctgttgtttgcctacccaattttctttcttttgctg--ataattcc--tttttcccatttgacaaagctgtatggttt-atttgtttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCTATAACTGATTCTGTAATTATGAAGGACAAGCATACTAAGATGCCTCGTGGATTTGGATTTGTTAC
















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|101402086|gb|EB822652.1|EB822652
EST:     AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
EST: gi|50336822|gb|CO531948.1|CO531948
EST:     AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
EST: gi|76014054|gb|DT941224.1|DT941224
EST:     AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
EST: gi|71417068|gb|DR803915.1|DR803915
EST:     AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
EST: gi|30088355|gb|CB886560.1|CB886560
EST:     TTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: TTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
EST: gi|211508855|gb|FL158319.1|FL158319
EST:     AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
EST: gi|76282448|gb|DV022016.1|DV022016
EST:     AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
EST: gi|71768840|gb|DR966777.1|DR966777
EST:     AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
EST: gi|71446122|gb|DR827172.1|DR827172
EST:     AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAG                         AATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA
genomic: AAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACTACTGAAGgtaaaattta ... ttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctgttctttccaaattgacaaatttgtatggttttatctgtttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAATTATGAAGGACAAGCATACTAAGATGCCTCGTGGATTTGGATTTGTTAC
                aattgac  putative branch site (score: 3)
                                        tctgttt  putative PPT
               aaattgacaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattttttcctgttcatctccaatccttggtttgctacttttgtgattctgttctttccaaattgacaaatttgtatggttttatctgtttgtatgtagAATCATTCTCCAAGCATTTTGAGAAGTATGGGGCAATAACTGATTCTGTAATTATGAAGGACAAGCATACTAAGATGCCTCGTGGATTTGGATTTGTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG