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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctctcccaatttaagcttcagttgttttgcaacttgggtatcttgttaaacaacaactttctggtatggtctctcccaattcttgcag

Basic information

species Zea mays
transcript GRMZM2G125556_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125556_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 5'ss of exon 6
ATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctctcccaattt-aagcttcagttgttttgcaacttgggtatcttgttaaacaacaactttctggtatggtctctcccaattcttgcag
|||||||||||||||||||||||| |||||||| || || ||||| |||||||| ||||||||||| |  ||||| |||||||| || ||  | |||||||||||| ||||| || ||| |||  | |||  ||| |     |   | |||  ||  |     |  |  |         ||   | ||||||||||
ATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctctcacattttgaaggcttagtcctttagtc-tgtaattgtctgattctaatgtgatgtcttc------catcatactattcttgcag
















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|76285485|gb|DV025053.1|DV025053
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
EST: gi|93282355|gb|EB674619.1|EB674619
EST:     AATTTTGCACGACCTTTTTTCCTTTCCTCAAAGAAAACCACAACTTTTTG                         GCGAGCGTCGGTCTTGATGATTTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
EST: gi|211377924|gb|FL095474.1|FL095474
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
EST: gi|71771167|gb|DR969104.1|DR969104
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
EST: gi|211249240|gb|FL481701.1|FL481701
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
EST: gi|60400894|gb|DN233701.1|DN233701
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
EST: gi|76283007|gb|DV022575.1|DV022575
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
EST: gi|211484414|gb|FL480094.1|FL480094
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
EST: gi|211475757|gb|FL124814.1|FL124814
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCT
EST: gi|211041270|gb|FL124817.1|FL124817
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAA-CCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATC
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATC
EST: gi|93282356|gb|EB674620.1|EB674620
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTG
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTG
EST: gi|161592264|gb|EY962319.1|EY962319
EST:     ATTTTGCACGACCTTCTCTCCTTTCCTCAAAAGAAAACCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATC
genomic: ATTTTGCACGACCTTCTCTCCTTTCCTCAAA-GAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATC
EST: gi|211466760|gb|FL298405.1|FL298405
EST:     AATTTTGCACGACCTTCTCTCCTTTCCTCNNNNNNNNCCACAACTTTCTG                         GCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT
genomic: AATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctc ... attcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTCCTCAAAGAAAACCACAACTTTCTGgtatggtctctcccaatttaagcttcagttgttttgcaacttgggtatcttgttaaacaacaactttctggtatggtctctcccaattcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA