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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactacactaaaattgtttccacttgagtcattctgtttgctgttcttgcggagaggatcacagaatttatataagcatctatctatttttgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG

Basic information

species Zea mays
transcript GRMZM2G085747_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os10g35960.1 (Oryza sativa), 3'ss of exon 16
-aactacactaaaattgtttccacttgagtcattctgtttgctgttcttgcggagaggatcacagaatttatataagca-tctatctatttttgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG
 || || |   |  |  |    |  | ||   ||           | | |     |      |   |  |||  |   | ||||   |||| ||  | ||||||| || ||||||||||||||||| |||||||||||||| |||||||| || ||  |||| ||
aaattagaacgatgtgatggaaaagttagaagtttgaagaaaaagtttggaactaaactcggcttgagctatgcatctaatctagtgatttctg--acgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG
















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|4647288|gb|AI622363.1|AI622363
EST:     TGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGNCGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|32933889|gb|CF038701.1|CF038701
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|71758667|gb|DR956604.1|DR956604
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|166461245|gb|EG146937.1|EG146937
EST:     TTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGA-TCCTCTTCCC
genomic: TTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|211281986|gb|FL018039.1|FL018039
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|74232917|gb|DT640831.1|DT640831
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|29130947|gb|CB381651.1|CB381651
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACAT
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACAT
EST: gi|76919652|gb|DV167818.1|DV167818
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|50334197|gb|CO529323.1|CO529323
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|40303330|gb|CK347717.1|CK347717
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|211050465|gb|FL475129.1|FL475129
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|213169886|gb|FM184059.1|FM184059
EST:     GCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: GCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|211281987|gb|FL018040.1|FL018040
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|4647287|gb|AI622362.1|AI622362
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|74232916|gb|DT640830.1|DT640830
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|74238357|gb|DT646271.1|DT646271
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|211326815|gb|FL454067.1|FL454067
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCMCAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|26456270|gb|CA827853.1|CA827853
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|78544875|gb|DV622373.1|DV622373
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|22819546|gb|BU499636.1|BU499636
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|30032196|gb|CB834047.1|CB834047
EST:     TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
genomic: TCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC
EST: gi|12971899|gb|BG267713.1|BG267713
EST:     CATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG                         CCTGGCATCATACATCACAGACGGCGAAATTCGAAAAGGAATCCTCTTCCC
genomic: CATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTGgtaagccttg ... tgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcggagaggatcacagaatttatataagcatctatctatttttgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG
                                     tctattttt  CT-rich tract
                   aatttatataagcatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactacactaaaattgtttccacttgagtcattctgtttgctgttcttgcggagaggatcacagaatttatataagcatctatctatttttgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA