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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgcatgttaaatggtatatggttttatgctcatgctattggtttattattttgctccatgatctaatcctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAATATTGGATCCTCCCTTCAATTTCCGATGTTGTTGTTGAGCAAG

Basic information

species Zea mays
transcript GRMZM2G179281_T01
intron # 2
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|74244789|gb|DT652703.1|DT652703
EST:     ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAG                         GTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
genomic: ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAGgtatttgcat ... cctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
EST: gi|211297396|gb|FL321272.1|FL321272
EST:     ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAG                         GTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
genomic: ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAGgtatttgcat ... cctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
EST: gi|50324484|gb|CO519610.1|CO519610
EST:     ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAG                         GTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
genomic: ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAGgtatttgcat ... cctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
EST: gi|32919451|gb|CF024263.1|CF024263
EST:     ACTTTCGCTCGAGGAAGCTGTACTTTACACCACATGCTGTTATTTACAAG                         GTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTTCAAAAAGGAGAAA
genomic: ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAGgtatttgcat ... cctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
EST: gi|71772785|gb|DR970710.1|DR970710
EST:     ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAG                         GTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
genomic: ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAGgtatttgcat ... cctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
EST: gi|50324921|gb|CO520047.1|CO520047
EST:     ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAG                         GTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA
genomic: ACTTTCGCTCGAGGAAGCTGTACTTGACACCGCATGCTGTTATTTACAAGgtatttgcat ... cctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgctcatgctattggtttattattttgctccatgatctaatcctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAATATTGGATCCTCCCTTCAATTTCCGATGTTGTTGTTGAGCAAG
                                            tcctaat  putative branch site (score: 2)
             tattggtttattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgcatgttaaatggtatatggttttatgctcatgctattggtttattattttgctccatgatctaatcctaatccagGTAAACAAGCCTTTTGCTTTTCCTTGTTTTGGAGTTTCCAAAAAGGAGAAATATTGGATCCTCCCTTCAATTTCCGATGTTGTTGTTGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG