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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttgagaccgtgattcttttatttgtatctatatagtgataatgtctttatttgataacattttgtaaccatttgtatgtgacacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAACATTATTGGAC

Basic information

species Zea mays
transcript GRMZM2G177575_T01
intron # 7
splice site 3'
intron type U2

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|148971473|gb|EE022167.2|EE022167
EST:     CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG                         GAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
genomic: CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAGgtactttgag ... acacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
EST: gi|149106837|gb|EE188735.2|EE188735
EST:     CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG                         GAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
genomic: CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAGgtactttgag ... acacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
EST: gi|86469449|gb|DY235819.1|DY235819
EST:     CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG                         GAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
genomic: CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAGgtactttgag ... acacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
EST: gi|78110126|gb|DV528541.1|DV528541
EST:     CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG                         GAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
genomic: CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAGgtactttgag ... acacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
EST: gi|78086094|gb|DV514487.1|DV514487
EST:     CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG                         GAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
genomic: CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAGgtactttgag ... acacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
EST: gi|76293066|gb|DV032634.1|DV032634
EST:     CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG                         GAACAGGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
genomic: CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAGgtactttgag ... acacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
EST: gi|213178693|gb|FM194771.1|FM194771
EST:     CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG                         GAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
genomic: CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAGgtactttgag ... acacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
EST: gi|211383908|gb|FL466788.1|FL466788
EST:     CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG                         GAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC
genomic: CTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAGgtactttgag ... acacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataatgtctttatttgataacattttgtaaccatttgtatgtgacacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAACATTATTGGAC
                          ttgtaac  putative branch site (score: 2)
                                              cacttcc  putative PPT
          tttatttgataacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttgagaccgtgattcttttatttgtatctatatagtgataatgtctttatttgataacattttgtaaccatttgtatgtgacacttccagGAACATGAGTATGTTTATTGCCTGGCAATCGTCAAGAGCATGAAGCTCAACATTATTGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA