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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctttactgcatttgattatcaacagctgtgcatgtttttagtgcgttcttgaatcaaatagctgaaagccaagaacataatttaatgagctac...

Basic information

species Zea mays
transcript GRMZM5G835235_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 2
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctttactgcatttgattatc----aacagctgtgcatgtttttagtgcgttcttgaatcaaatagctg----aaagccaagaacataatttaatgagctac----------------
||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || ||||||| || | | | |   ||| |  | ||     ||||  ||  ||| |   |   ||| |||  |||     | |      ||||| |    |||   | | |||  | |                
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccatgttgtgatttcagaacaaatgc-catctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcag

upper sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g14860.4 (Oryza sativa), 5'ss of exon 3
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctttactgcatttgattatc----aacagctgtgcatgtttttagtgcgttcttgaatcaaatagctg----aaagccaagaacataatttaatgagctac--------------------
||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || ||||||| || | | | |   ||| |  | ||     ||||  ||  ||| |   |   ||| |||  |||     | |      ||||| |    |||   | | |||  | |                    
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccatgttgtgatttcagaacaaatgc-catctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcagacag
















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|13490381|gb|BG517145.1|BG517145
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACA
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACA
EST: gi|67039601|gb|CO465856.1|CO465856
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|22819758|gb|BU499848.1|BU499848
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|211304795|gb|FL143344.1|FL143344
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|87156577|gb|DY401366.1|DY401366
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|211304794|gb|FL143343.1|FL143343
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|24773942|gb|CA409196.1|CA409196
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|26559736|gb|CA831971.1|CA831971
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|32865540|gb|CF005222.1|CF005222
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|32931957|gb|CF036769.1|CF036769
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|32933926|gb|CF038738.1|CF038738
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctttactgcatttgattatcaacagctgtgcatgtttttagtgcgttcttgaatcaaatagctgaaagccaagaacataatttaatgagctac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagaaca