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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtatacctttgctcttcatgctgctcatgactaccttttcacccagtcttaatttcaacctgccaggtattttccactgtctcttcgttatgacctgtatcaattaatgcag

Basic information

species Zea mays
transcript GRMZM2G017525_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 5'ss of exon 8
GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtatacctttgctcttcatgctgctcatgactaccttttcacccagtcttaatttcaacctgccaggtattttccactgtctcttcgttatgacctgtatcaattaatgcag
||||||||||||||||||||||| ||||| ||||| ||||||||||| ||| |||||||||||||| |||||||||   ||  |     |||   ||||| |    |||    |    | ||||||          | |||||| | ||| ||||||| || ||| ||| ||||| |    |||
GGAGAAATGCAGCAACTCCGGGATAAACTGGCTATAGCAGAAAGGGCCGCACGATCAGAAGCTCAATTGAAAgtatgttttgac-----atgt--ctcataaagttcttccatcttcctgttaatt----------atgtattt-ctactatctcttcattgtgatctgcatcaaatttctcag

upper sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 8
GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgta--tacctttgctcttcatgctgctcatgactaccttttcacccagtcttaatttcaacctgccaggtattttccactgtctcttcgttatgacctgtatcaattaatgcag
|| ||||||||||||||| ||||||| ||||||||  | |||||  |||||| ||| ||||| ||| ||||||||  ||  ||   | ||||   |   |||| |||        | | |   || |||| || ||   | | ||    |  |    || |   ||  ||||              
GGGGAAATGCAGCAACTCAGGGACAAGCTTGCTATAACGGAAAGAACTGCAAAATCTGAAGCACAATTGAAAgtaaataatttgctttttcagaatatacatgtctaa------gctctgcaatattttccacatg---gttcttgaaaatagaacttttgaattgtactgtgcag----------
















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|20803194|gb|BQ294244.1|BQ294244
EST:     ACAAACTTGCTATTGTTTAAAGGGCTGTAAGATCAGAAGCTCAACTGAAA                         GAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
genomic: ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtataccttt ... attaatgcagGAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
EST: gi|18660383|gb|BM500833.1|BM500833
EST:     ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA                         GAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
genomic: ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtataccttt ... attaatgcagGAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
EST: gi|23199547|gb|BU582112.1|BU582112
EST:     ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA                         GAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
genomic: ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtataccttt ... attaatgcagGAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
EST: gi|67023844|gb|CO452593.1|CO452593
EST:     ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA                         GAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
genomic: ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtataccttt ... attaatgcagGAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
EST: gi|22521576|gb|BU080387.1|BU080387
EST:     ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA                         GAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
genomic: ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtataccttt ... attaatgcagGAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
EST: gi|6859889|gb|AW355883.1|AW355883
EST:     ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA                         GAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
genomic: ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtataccttt ... attaatgcagGAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
EST: gi|26456327|gb|CA827910.1|CA827910
EST:     ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAA                         GAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT
genomic: ACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtataccttt ... attaatgcagGAGAAGTTCCAGCTACGACTTAAGGTACTCGAGGAAGGATTGAGAATGTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGAAATGCAGCAACTCCGGGACAAACTTGCTATTGCAGAAAGGGCTGCAAGATCAGAAGCTCAACTGAAAgtatacctttgctcttcatgctgctcatgactaccttttcacccagtcttaatttcaacctgccaggtattttccactgtctcttcgttatgacctgtatcaattaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA