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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtgtatttcctgaagagatctgatgggtctggactgctttcctagtttcctagacaccgtattccattgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCATCTTGAGCAGAATCAGCTTACCGATGCACTATCTTGTTTGGACGAAGCAT

Basic information

species Zea mays
transcript GRMZM2G150772_T01
intron # 19
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|50327860|gb|CO522986.1|CO522986
EST:     CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAG                         GTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
genomic: CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAGgtactgtgta ... attgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
EST: gi|211235808|gb|FL257327.1|FL257327
EST:     CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAG                         GTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
genomic: CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAGgtactgtgta ... attgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
EST: gi|50333207|gb|CO528333.1|CO528333
EST:     CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAG                         GTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
genomic: CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAGgtactgtgta ... attgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
EST: gi|67020588|gb|CO449337.1|CO449337
EST:     CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAG                         GTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
genomic: CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAGgtactgtgta ... attgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
EST: gi|149039486|gb|EE046628.2|EE046628
EST:     CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAG                         GTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
genomic: CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAGgtactgtgta ... attgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
EST: gi|78179500|gb|DV549873.1|DV549873
EST:     CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAG                         GTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
genomic: CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAGgtactgtgta ... attgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
EST: gi|149075857|gb|EE164402.2|EE164402
EST:     CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAG                         GTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT
genomic: CGAAGCAAGCTGCTCGCCCTCCAGCACCTACTGCTGTGCGGCCTGGCCAGgtactgtgta ... attgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgggtctggactgctttcctagtttcctagacaccgtattccattgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCATCTTGAGCAGAATCAGCTTACCGATGCACTATCTTGTTTGGACGAAGCAT
 atctgat  putative branch site (score: 4)
                                         ttccatt  putative PPT
                                             attgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtgtatttcctgaagagatctgatgggtctggactgctttcctagtttcctagacaccgtattccattgttacagGTACCACGCGGGGCCCCTGCTGCAGAATGCTACAAGATGGCTCTTGCTCATCTTGAGCAGAATCAGCTTACCGATGCACTATCTTGTTTGGACGAAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT