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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttgttacttgctccacagttccagtctttcgtatttgaaatgctgactgctgttcagctgttagccgaggcaaatgtagcatcattcagagctaaatatcccgtgcttttcagagtgtaatcctgcgtcttctttgagtgcag

Basic information

species Zea mays
transcript GRMZM2G004352_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g54640.2 (Oryza sativa), 5'ss of exon 3
ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttgttac-ttgctccacagt---------------tccagtctttcgtat-ttgaaatgctg-actgctgttcagctgttagcc--gaggcaaatgtagcatcatt-------cagagc-----taaatatcccgtgctt--ttcagag-tgtaatcctgcgtcttctttgagtgcag--------
|||||||| || |||||||| || ||||| || ||||| ||||||||  | || ||||| ||||| ||||||||||| ||  ||| |||   |||  | | |               |  |||  || | |  ||| |||| || |  |   ||  |  |  |  |  ||  |||   | |||  |||       ||||       ||    | || |  ||  ||||||    ||||||||| | ||| |||  ||           
ACATCTCTGCGAGAGCTCACCACGCTTGGGATAAAGAACGCTGAGAACCTGGCGATTCCGAGTGTCAGAAATGATgtaaggcttgctacacagcttaaaaatgtatctgtaactttgtttagttatttgcaaattgcaatggtgcaacgtgattttgtgggaattctggaatcaagcattgcaaaattgcatatgcagaagaatagtagtagtgccataatttgttcagaaacataatcctgcattttccttgt-tgtgatcatgcag

upper sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 5'ss of exon 3
ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttgttacttgctccacagttccagtctttcgtatttgaaatgctgactgctgttcagctgttagccgaggcaaatgtagcatcattcagagctaaatatcccgtgcttttcagagtgtaatcctgcgtcttctttgagtgcag
|||||||| |||||||| || ||||||||||| |||||||| || ||  | |||||||||||||||||||||||||| ||| ||   ||     |      ||||  |||  | | ||       ||| ||      |||  |    | |     || |  || |  ||| | |   | |   | |  |                                    
ACATCTCTTCGGGAGCTGACAACCCTTGGAATGAAGAATGCGGAAAACCTTGCAATTCCAAGTGTTAGAAATGATgtaagtattagaaca----ctgataatcca--cttgaggacttattgcattgagtg------agcattccatcaactagtatttgtcacc--tcatatccttacagttcctatt------------------------------------
















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|211057845|gb|FL422564.1|FL422564
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCAC
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCAC
EST: gi|50329898|gb|CO525024.1|CO525024
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|211212631|gb|FL412327.1|FL412327
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|148954649|gb|EC900096.2|EC900096
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|149084909|gb|EE174419.2|EE174419
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|211463633|gb|FL380567.1|FL380567
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|211057978|gb|FL426568.1|FL426568
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|211087785|gb|FL400777.1|FL400777
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|71313543|gb|DR793346.1|DR793346
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|211403691|gb|FL424169.1|FL424169
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGG
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGG
EST: gi|211110152|gb|FL388603.1|FL388603
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|211493014|gb|FL369799.1|FL369799
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGAATCTTAGCCGTCC
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCC
EST: gi|37417290|gb|CF646298.1|CF646298
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|211472091|gb|FL427745.1|FL427745
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|148930743|gb|EC873038.2|EC873038
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT                         GCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT
genomic: TTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttg ... ttgagtgcagGCGGCATTCTTGTTTACAGTTGTGGGTACCACTGGATTCTTAGCCGTCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGATgtgagtgttgttacttgctccacagttccagtctttcgtatttgaaatgctgactgctgttcagctgttagccgaggcaaatgtagcatcattcagagctaaatatcccgtgcttttcagagtgtaatcctgcgtcttctttgagtgcag

- - - - - - - - - - - - - - - - - -  ATGCTG