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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagcttctgtttctatgttaatcactgttgctcgcgttggggaaatgttaattgtccatttcgatgtgattgtggtggcgttag

Basic information

species Zea mays
transcript GRMZM2G086052_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086052_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g40620.1 (Oryza sativa), 5'ss of exon 2
AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagcttctg----------tttctatgttaatcactgttgctcgc--gttggggaaatgttaattgtccatttcgatgtgattgtggtggcgttag
||||||||||||||||||||||||| |||||||| || |||||| |||||||||||||||||||| | |||  |           | |   || ||||| ||  || | ||   |  || |||||| | |||    | |  |  |  |  |   |  |||||
AGCACTCGCACGAGCCGTCGTCGGATTCCGAGCTAGTGAAGCACCTCAAGAGCATCATAAAGgtgtccgctgtttataatgagcctcttcgtgataatctctactgtttgccaatgcggaaaatgtgatttggtgttgtgaaaattgtgattcggaggttag
















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|71326245|gb|DR799816.1|DR799816
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|32792113|gb|CD944349.1|CD944349
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|32826797|gb|CD966475.1|CD966475
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAACATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|93016466|gb|EB641986.1|EB641986
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|71297897|gb|DR784919.1|DR784919
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|93281358|gb|EB673622.1|EB673622
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|78108018|gb|DV526436.1|DV526436
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|71313522|gb|DR793329.1|DR793329
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|94478202|gb|EB707160.1|EB707160
EST:     CCCGTCGTCGGAATCCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCCGGAGTGGGCCACTCAGCCTAGCTGAATACATGGAGGAGGCGCTGAC
genomic: GCCGTCGTCGGAATCC-GAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTC-GGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGAC
EST: gi|71297664|gb|DR784782.1|DR784782
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|149097668|gb|EE183570.2|EE183570
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|93281137|gb|EB673401.1|EB673401
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|76293021|gb|DV032589.1|DV032589
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|32824168|gb|CD963890.1|CD963890
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|78090509|gb|DV518883.1|DV518883
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|89251237|gb|DY623023.1|DY623023
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
EST: gi|71772608|gb|DR970536.1|DR970536
EST:     AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG                         TTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG
genomic: AGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagctt ... gtggcgttagTTTCGGAGTGGGCCAATCAGCATAGCTGAATACATGGAGGAGGTGCTGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAGgtgccagcttctgtttctatgttaatcactgttgctcgcgttggggaaatgttaattgtccatttcgatgtgattgtggtggcgttag

- - - - - - - - - - - - - - - - - - - - - - - - AGAGCA