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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCGATCCCACTGGCGAGGCTTGGGTGTCTGTGTTCAATGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaatactccggactgacagcattggatttcttctgtttctttgtttgccttgcccctgacagtgggctcgccgtttgtttgcag

Basic information

species Zea mays
transcript GRMZM2G086934_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086934_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 5'ss of exon 11
CTCCGATCCCACTGGCGAGGCTTGGGTGTCTGTGTTCAATGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaatactccggactgacagcattggatttcttctgtttctttgtttgccttgcccctgacagtgggctcgccgtttgtttgcag------------
|||||| || ||||| ||||| ||| | ||| |||||||||| || ||||||| |||  |||||||||| || || |||||||||||||| ||||| ||||||| ||    | |||        | | |||  |  | |  || |   |  | | |||     | ||  || ||         |  || ||            
CTCCGACCCTACTGGTGAGGCCTGGCTTTCTCTGTTCAATGATCAGGCAGAGAGGATTGTTGGCTGCAGTGCAGATGAGCTTGATCGGATTAGGAAGGAGgtaattttgccaatccca--cagtaactttgattcaccttcgtgtaaattctaggctttagtttaactttgtgcgaatt-ccaggctgtagttcaagcttgtg
















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|84970001|gb|DW468385.1|DW468385
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|110521782|gb|EE025966.1|EE025966
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|7238099|gb|AW573471.1|AW573471
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|32929843|gb|CF034655.1|CF034655
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|67028077|gb|CO456826.1|CO456826
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|211227170|gb|FL464276.1|FL464276
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|149086432|gb|EE175975.2|EE175975
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|74239181|gb|DT647095.1|DT647095
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|67023291|gb|CO452040.1|CO452040
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAA                         GANGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|211375733|gb|FL457574.1|FL457574
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|60342386|gb|DN209359.1|DN209359
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|211223034|gb|FL464238.1|FL464238
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|166706468|gb|EG124347.1|EG124347
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCC
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaa ... ttgtttgcagGAGGGGGACGACAGCTACGTTCTCAAGCTCAAGGAAGCCACCTGGGTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCGATCCCACTGGCGAGGCTTGGGTGTCTGTGTTCAATGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattcaatactccggactgacagcattggatttcttctgtttctttgtttgccttgcccctgacagtgggctcgccgtttgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT