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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtggcaagaacaaattcactagattaaattctcttcacactttttaagttctgtagctattttgtctctttatagtaacaccatacttatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC

Basic information

species Zea mays
transcript GRMZM2G101413_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101413_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 3
-----catgtgg-caagaacaaattcactagattaaattctcttcacactttttaagttctgtagctattttgtctctttatagtaacaccatacttatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC
      ||  ||   ||  ||   |    | | | ||   ||  ||  ||| | | ||||     | | || ||||||||  |||  ||| |||||| |||| ||||||||||||||| |||||||| |||||||||||||| ||||| ||||| |||||||| | ||||||||||||||
gtccagattcggattagggcatgctttaaatagtgaacgatcgacatgcttct-aggttc-----ccagttggtctctttcaagtctcacaatacttgttttgcagGGCCTACCGTGCATTTTACATCCTAAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC

upper sequence: GRMZM2G101413_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 3
--catgtggcaagaacaaat-tcac-tagattaaattctcttcacactttttaagttctgtagctattttgtctctttatagtaac-accatacttatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC
  ||  ||     | || || |||| ||    |||        | |||| |    ||   ||  || ||||        |   ||| |  ||| | | | | ||||||||| ||||| || ||||| || ||||||||||| |||||||||||||||   |||   ||| |||||||  
aacacatgtttgcaccatatatcacataagcaaaaagagacataaacttgt---atttaata--tactttgggataaacttccaactaatatattcaatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGAGCAACATTTTAGCCGATGGATAG
















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|149082454|gb|EE171644.2|EE171644
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|76914884|gb|DV165734.1|DV165734
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|12971772|gb|BG267650.1|BG267650
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|71332207|gb|DR803027.1|DR803027
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|91874972|gb|EB404929.1|EB404929
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCCCGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|76014786|gb|DT941956.1|DT941956
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|71332206|gb|DR803026.1|DR803026
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTTTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|18181443|gb|BM382653.1|BM382653
EST:     TAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: TAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|87157131|gb|DY401920.1|DY401920
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|101390410|gb|EB817139.1|EB817139
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTGCCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|113702315|gb|EE679819.1|EE679819
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|211107241|gb|FL370796.1|FL370796
EST:     AGAAGCAGAGATGTGGATAACTTAACTGGACAATATGTTTTCCTCCGTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCNGT-ATTTCACGG
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATC-GTTATTTCACGG
EST: gi|18180216|gb|BM381426.1|BM381426
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|211215315|gb|FL417122.1|FL417122
EST:     AGAA-CAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGGCTACCGTGCGTTTTCCATTCTAA-CTGGATT-ATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|211199199|gb|FL385609.1|FL385609
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|211009339|gb|FL418571.1|FL418571
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|76012114|gb|DT939284.1|DT939284
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|211060163|gb|FL397358.1|FL397358
EST:     GAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCNTTGG                         GGCCTACCGTGCGTTTTACAT-CTAAACTGGATTTATCCGT-ATTTCACG
genomic: GAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCC-TTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATC-GTTATTTCACG
EST: gi|149082455|gb|EE171645.2|EE171645
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|50332292|gb|CO527418.1|CO527418
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|211299206|gb|FL414893.1|FL414893
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|148943936|gb|EC889016.2|EC889016
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|74243070|gb|DT650984.1|DT650984
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|4647085|gb|AI622160.1|AI622160
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGNCAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|67014344|gb|CO443093.1|CO443093
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|60358513|gb|DN225486.1|DN225486
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|148943937|gb|EC889017.2|EC889017
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|9743078|gb|BE519226.1|BE519226
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGCCAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCCACGG
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTT-CACGG
EST: gi|211119295|gb|FL407774.1|FL407774
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGNTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|76012125|gb|DT939295.1|DT939295
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|148990937|gb|EE032363.2|EE032363
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
EST: gi|101390412|gb|EB817140.1|EB817140
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtacgttttt ... tatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagttctgtagctattttgtctctttatagtaacaccatacttatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC
                              tagtaac  putative branch site (score: 1)
                                           cttatttttc  putative PPT
                                        atacttatttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtggcaagaacaaattcactagattaaattctcttcacactttttaagttctgtagctattttgtctctttatagtaacaccatacttatttttcagGGCCTACCGTGCGTTTTACATTCTAAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA