Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatattttcttccatgatttattgtttcatgtgcatccagccttggcactgtgcatcaagaaaatatttaccacattatttcatcttttgatataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGGCAATGGTCGCTTTTTCAACCTCA

Basic information

species Zea mays
transcript GRMZM2G155662_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155662_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g05350.1 (Oryza sativa), 3'ss of exon 3
tatattttcttccatgatttattgtttcatgtgcatccagcctt-ggcactgtgcatcaagaaaatatttaccacattatttcatcttttgat----ataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGGCAATGGTCGCTTTTTCAACCTCA
  || |||||| ||| ||||| |   |   |||||| |    || ||   |||||||| | |||  ||||         |||  |  ||  ||    | | | || || |||||||||||||| |||||||||||| ||||||||||||||||||||||  ||||||||||||| ||||
--tagtttctttcattatttactacct---gtgcattcttttttcggttttgtgcatcgataaataatttgtttatcctttttgttgttccatcttcaaacatagTGATGAAGGTAAAGTGCGGAAGGTTCTAAAAGTTGAGCCAACACCAGATGGCAACAGTCGCTTTTTCAATCTCA
















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|71448588|gb|DR829638.1|DR829638
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|91877076|gb|EB407033.1|EB407033
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCCAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCCACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|30087546|gb|CB885752.1|CB885752
EST:     CAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACCCCAGATGG
genomic: CAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|71427013|gb|DR808063.1|DR808063
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|93015159|gb|EB640679.1|EB640679
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|89253003|gb|DY624789.1|DY624789
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|76019636|gb|DT946806.1|DT946806
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|78078777|gb|DV507189.1|DV507189
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|71311953|gb|DR792477.1|DR792477
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|76926154|gb|DV170738.1|DV170738
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|71325427|gb|DR799398.1|DR799398
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|91050359|gb|EB160777.1|EB160777
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|89247407|gb|DY619193.1|DY619193
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|20301062|gb|BQ164005.1|BQ164005
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|76925400|gb|DV170433.1|DV170433
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|91054380|gb|EB164798.1|EB164798
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|78075431|gb|DV503865.1|DV503865
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|31909099|gb|CD650749.1|CD650749
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|76925466|gb|DV170456.1|DV170456
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCCAAC-CCAGATG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCC-AACACCAGATG
EST: gi|50336696|gb|CO531822.1|CO531822
EST:     GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: GGTCCAACAGATTCATGCGAGTTCTTTCATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
EST: gi|71762896|gb|DR960833.1|DR960833
EST:     CATGACCCTTTCAAGGGGCGGAG                         CGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG
genomic: CATGACCCTTTCAAGGGGCGGAGgttggtatca ... atataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcactgtgcatcaagaaaatatttaccacattatttcatcttttgatataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGGCAATGGTCGCTTTTTCAACCTCA
                                        ttttgat  putative branch site (score: 4)
                             attatttcatcttttg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatattttcttccatgatttattgtttcatgtgcatccagccttggcactgtgcatcaagaaaatatttaccacattatttcatcttttgatataaacagCGAAGAAGGTAAAGTGCGTAAGGTTCTAAAAATTGAGCCAACACCAGATGGCAATGGTCGCTTTTTCAACCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG