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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatgagtgccaaacagctcctttccatgggcttgatcatatatgcacatgtattttatagtggccactgactgcagtgttcctgaaatactttgtaaactcaaaatctgcattttgcttgggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTCACATTTCTCAGGTTTTGCAAGCAGCTGGCTGAGGGTGCATGGGCAGTAG

Basic information

species Zea mays
transcript GRMZM2G026643_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026643_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g45250.1 (Oryza sativa), 3'ss of exon 5
gtgagatgagtgccaaacagctcctttccatgggcttgatcatatatgcacatgtattttatagtggccactgactgcagtgttcctgaaatactttgtaaactcaaaatctgcattttgcttgggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTCACATTTCTCAGGTTTTGCAAGCAGCTGGCTGAGGGTGCATGGGCAGTAG
      |||||||  | || |         ||    || |||| ||| |  |  || | ||    |     |  ||    | ||         |||| | || |   ||| |   || || |||  ||||||||||||||||||||||||||||||||||||||||||| || || |||||||| ||||||||| ||||||| |||||||||||||||||||||||||||||||
-----gtgagtgctgatcaaca-------gtgctaatgttcatttat-cttacatagtgtaagacg-----tagctaacatatttt-------ctttctgaattgttaatttttcttgtgtttgcttgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTACCAATTAGGGAGGTTACATTTCTCCGGTTTTGTAAGCAGCTGGCTGAGGGTGCATGGGCAGTAG
















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|211456522|gb|FL289841.1|FL289841
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022955|gb|FL081004.1|FL081004
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022960|gb|FL081009.1|FL081009
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211456527|gb|FL289846.1|FL289846
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022956|gb|FL081005.1|FL081005
EST:     GACATCTGGCATTGCAGGAAGTANGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: GACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022959|gb|FL081008.1|FL081008
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022962|gb|FL081011.1|FL081011
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022953|gb|FL081002.1|FL081002
EST:     GAGGTGACATCTGGCATTGCMGGAAGTTGGGAATGGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: GAGGTGACATCTGGCATTGCAGGAAG-TAGGAAT-GGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022958|gb|FL081007.1|FL081007
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211456521|gb|FL289840.1|FL289840
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022951|gb|FL081000.1|FL081000
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211418991|gb|FL080999.1|FL080999
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022963|gb|FL081012.1|FL081012
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211456524|gb|FL289843.1|FL289843
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|211022957|gb|FL081006.1|FL081006
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|149072468|gb|EE160744.2|EE160744
EST:     AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: AGGAGGTGACATCTGGCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
EST: gi|50333151|gb|CO528277.1|CO528277
EST:     GCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTG                         ATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC
genomic: GCATTGCAGGAAGTAGGAATGGTGCGCTGCTGCTGgtgagatgag ... ggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttcctgaaatactttgtaaactcaaaatctgcattttgcttgggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTCACATTTCTCAGGTTTTGCAAGCAGCTGGCTGAGGGTGCATGGGCAGTAG
         aaatactttgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatgagtgccaaacagctcctttccatgggcttgatcatatatgcacatgtattttatagtggccactgactgcagtgttcctgaaatactttgtaaactcaaaatctgcattttgcttgggtgcaacagATGAAGGCTGAGCTACAGGTGCTCTCACCTCTAGTGCCCATCAGGGAGGTCACATTTCTCAGGTTTTGCAAGCAGCTGGCTGAGGGTGCATGGGCAGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG