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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatttctctaattcactgtttactgcctctccttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG

Basic information

species Zea mays
transcript GRMZM2G146206_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaattt-----ctctaattcactgtttactgcctctccttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG-----
  |  |    |||  ||||   |  |||       || || ||    | ||||| | ||      | |||| |   ||| |  |    ||| |  | |||| |||| || ||||| |||||||| ||| |||| ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||     
--tctttatggct--tttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtctttt-ttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT

upper sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatt-----tctctaattcactgtttactgcctctccttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG
  |  |    |||  ||||   |  |||       || || ||    | ||||| | ||      | |||| |   ||| |  |    ||| |  | |||| |||| || ||||| |||||||| ||| |||| ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||
--tctttatggct--tttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtctttt-ttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG

upper sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatttctctaattcactgtttactgcctctccttttgt---tttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG
  |   |    ||| | | |   ||  |    ||       ||        |    ||||   ||     || | |  |  ||  ||||  ||   |||||||  ||||||||| |||||   ||| | || ||||| ||||| ||||||||||| ||||| || || || ||||||||||||||||||||||| |||
gttaaaaaaaactgttctaa---ttgctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG

upper sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G04290.2 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------cattctagctgctgctttgaa----------ttttattccttcacgcagaaatgagggacttctga------atttctctaattcactgtttactgcctctcctt--ttgt-tttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG-----
                                                                              | ||   | |  || ||  ||            | ||| ||| |       || |    ||  | |      ||||   ||     || | |  |  ||  ||||  |||| |||||||  ||||||||| |||||   ||| | || ||||| || || ||||||||||| ||||| || || || ||||| ||||||||||||||||| |||     
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgctattttgttagcaatctatattttcgctgaccttaattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAGGTATG

upper sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G04290.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------cattctagctgctgctttgaa----------ttttattccttcacgcagaaatgagggacttctga------atttctctaattcactgtttactgcctctcctt--ttgt-tttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG
                                                                              | ||   | |  || ||  ||            | ||| ||| |       || |    ||  | |      ||||   ||     || | |  |  ||  ||||  |||| |||||||  ||||||||| |||||   ||| | || ||||| || || ||||||||||| ||||| || || || ||||| ||||||||||||||||| |||
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgctattttgttagcaatctatattttcgctgaccttaattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAG

upper sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
-cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatttctctaattcactgtttactgcctctcc-ttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG
  |    |  |  |  || |     ||| ||||    |  |  ||   |  ||||  ||      |  |   || | | |   |  |  |||| | || |||||||| | |||   |||   |||||||| ||||| |||||||| |||||||| ||||| || || || |||||||| ||||||||||| ||||| 
ctacatgaatttgtaatt-gtgccatatcccttttttct-agctgtatgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA

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|31352539|gb|CD436896.1|CD436896
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|16919933|gb|BM074427.1|BM074427
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|14243822|gb|BG841520.2|BG841520
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|24767602|gb|CA402746.1|CA402746
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|149005098|gb|EE039627.2|EE039627
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|24769561|gb|CA404690.1|CA404690
EST:     AATGGATGTTGTTGCTGCCCAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: AATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|71757929|gb|DR955866.1|DR955866
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|16927318|gb|BM080387.1|BM080387
EST:     AGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: AGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|149105683|gb|EE291241.2|EE291241
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|32909130|gb|CF013942.1|CF013942
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|6012502|gb|AW061939.1|AW061939
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|149097485|gb|EE183357.2|EE183357
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|211291624|gb|FL459848.1|FL459848
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGNATGTGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|148995362|gb|EE034576.2|EE034576
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|110517584|gb|EE022171.1|EE022171
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         N
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcag-
EST: gi|110517584|gb|EE022171.1|EE022171
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         N
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcag-
EST: gi|83278303|gb|DV942311.1|DV942311
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|16927255|gb|BM080324.1|BM080324
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|18178250|gb|BM379460.1|BM379460
EST:     ATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: ATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|71330644|gb|DR802095.1|DR802095
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|211297519|gb|FL438922.1|FL438922
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|211376603|gb|FL163143.1|FL163143
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAAATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|31628067|gb|CD526427.1|CD526427
EST:     GGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
EST: gi|110960987|gb|EE181039.1|EE181039
EST:     GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTG                         AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG
genomic: GGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaactttta ... tgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggacttctgaatttctctaattcactgtttactgcctctccttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG
               ctctaat  putative branch site (score: 3)
                            tttactgcctctcctt  putative PPT
                                          ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatttctctaattcactgtttactgcctctccttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG