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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcccctttatcatagatcgtgttatctagattcgtgtctacattcttcatgtgcttatttctaagaagcacacgattgcaatgttctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG

Basic information

species Zea mays
transcript GRMZM5G896082_T01
intron # 9
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|50332707|gb|CO527833.1|CO527833
EST:     CCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAA                         TTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
genomic: CCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAAgtatgcccct ... ctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
EST: gi|149111106|gb|EE294602.2|EE294602
EST:     ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAA                         TTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
genomic: ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAAgtatgcccct ... ctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
EST: gi|78092903|gb|DV521277.1|DV521277
EST:     ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAA                         TTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
genomic: ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAAgtatgcccct ... ctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
EST: gi|93014353|gb|EB639873.1|EB639873
EST:     ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAA                         TTGCAGTACCGAGCTGGAATATGACTCANAATCTCGGGTGATCACACTTCC
genomic: ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAAgtatgcccct ... ctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
EST: gi|71763483|gb|DR961420.1|DR961420
EST:     ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAA                         TTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
genomic: ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAAgtatgcccct ... ctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
EST: gi|13516143|gb|BG518419.1|BG518419
EST:     ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAA                         TTGCAGTACCGAGCTGGAATATGACTC
genomic: ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAAgtatgcccct ... ctatttccagTTGCAGTACCGAGCTGGAATATGACTC
EST: gi|149058762|gb|EE156780.2|EE156780
EST:     ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAA                         TTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC
genomic: ATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAAgtatgcccct ... ctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcttcatgtgcttatttctaagaagcacacgattgcaatgttctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG
                                           ttctatttcc  CT-rich tract
              ttatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcccctttatcatagatcgtgttatctagattcgtgtctacattcttcatgtgcttatttctaagaagcacacgattgcaatgttctatttccagTTGCAGTACCGAGCTGGAATATGACTCAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC