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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATGACATAACAAGCATAATCAGCTCATTGTACTACAAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagtctagttgcataatatatgcctaatttcacgttacttgtatcagcatttatgttcaacgtccactgtttacttgttcag

Basic information

species Zea mays
transcript GRMZM5G825226_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825226_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g56230.2 (Oryza sativa), 5'ss of exon 3
GCTTATGACATAACAAGCATAATCAGCTCATTGTACTACAAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagtctagttgcataatatatgcctaatttcacgttacttgtatcagcatttatgttcaacgtccactgtttacttgttcag-
|  |||||||| |||  | ||||||| |||||||||||||||||||||||||| ||||| |||| |||||||||||||||||||||||||| || |||| |  ||| | ||| |||| |  |||||||| ||  | | ||          || ||| |||||  | ||  ||||    
GTCTATGACATCACACACTTAATCAGTTCATTGTACTACAAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAGgtgaagcagtgtgtttgtagaatttatgtcctatttcacgctatatttgtct---------tttaacttccaccttctaactgttttag

upper sequence: GRMZM5G825226_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g56230.5 (Oryza sativa), 5'ss of exon 3
GCTTATGACATAACAAGCATAATCAGCTCATTGTACTACAAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagtctagttgcataatatatgcctaatttcacgttacttgtatc----agcatttatgttcaacgtccactgtttacttgttcag--------------------------------
|  |||||||| |||  | ||||||| |||||||||||||||||||||||||| ||||| |||| |||||||||||||||||||||||||| || |||| |  ||| | ||| |||| |  |||||||| ||  | | ||    | | |  |  ||| |  |    |     | ||| ||                                 
GTCTATGACATCACACACTTAATCAGTTCATTGTACTACAAGGGTTATGGTTCTCTTACGAAAATCCAAAAGCTTGAGTGGAACAACAGgtgaagcagtgtgtttgtagaatttatgtcctatttcacgctatatttgtcttttaacttccaccttctaactgttttaggggcatgtccactgtccatgcaatgtttatcacattaatgtcag
















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|149069941|gb|EE158341.2|EE158341
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|26455029|gb|CA826612.1|CA826612
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|148934690|gb|EC878738.2|EC878738
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|71771875|gb|DR969812.1|DR969812
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|76925225|gb|DV170328.1|DV170328
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|21330525|gb|BQ485906.1|BQ485906
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|78082331|gb|DV510743.1|DV510743
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|78112273|gb|DV530667.1|DV530667
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|74237536|gb|DT645450.1|DT645450
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|149078049|gb|EE166790.2|EE166790
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|76918369|gb|DV167265.1|DV167265
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
EST: gi|28566726|gb|CB278374.1|CB278374
EST:     AGGGCTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAG
genomic: AGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGG-AACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAG
EST: gi|87154553|gb|DY399342.1|DY399342
EST:     AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAG                         GGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT
genomic: AAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagt ... acttgttcagGGGCATGTCCACTATCCATGCGATATTCATCACAGTGGTGTCAGTGTACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATGACATAACAAGCATAATCAGCTCATTGTACTACAAGGGTTATGGTTCACTTACAAAAACCCAAAAGCTTGAGTGGAACAACAGgtcaaacagtctagttgcataatatatgcctaatttcacgttacttgtatcagcatttatgttcaacgtccactgtttacttgttcag

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