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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttttttttgtatagtgacttttttttggcttccaataatcctctatcctccaaattcaattacttataacagttatggattctcatagttaacctcgaatattcttcaactacag

Basic information

species Zea mays
transcript GRMZM2G099255_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099255_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 5'ss of exon 6
CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttttttttgtatagtgacttttttttggcttccaa--taatcctctatcctccaaattcaattact--tataacagttatggattctcatagttaacctcgaatattcttca--actacag------------------------------------------------------------------
 ||||| ||||||||||||||||||||||| ||||||||||| |||||||||||||||||||| |||| |||||||||||| ||||| ||||| ||| |||  | || ||| |   | |     |  || |||  |  | || |  | |   | ||   |  ||  || ||  |||  |          ||  | ||  |||| || |    | || |                                                                   
TTTTGACGATCCTGGTCCACATGGAGCAGGCAGATATTCTGATCATATGCTACCTGAAATTGTTAAGAGAGATTGGAGAAAAGGTGCACAGgt-atactttaatatgcataatttttctagaaagtattgcaaactgttgctttgccttttcattttcttcccttttacaaatgtttagagcgggtgctgtggaacttcaataatcctgggtattatactctaaagaattgctatattgtcatacagtctaacctcacacattctgatatgttttcctcttgcag

upper sequence: GRMZM2G099255_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G19160.1 (Arabidopsis thaliana), 5'ss of exon 6
CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttttttttgtatagtgacttttttttggcttccaataatcctctatcctccaaattcaattacttataacagttatggattctcatagttaacctcgaatattcttcaactacag
||||||||||||||||||||||||| | || ||  ||   || || ||| | || ||||||   | | ||||||   |||||||||| |||||       | |   ||||  | |  ||  ||     ||  | || | | |||    | |  ||| | |  || ||  | |   |||      | | ||    |  |  |  |         
CTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAGgta------tgtccagtat--taatcttgcttcatactctga-aaacatatatg---cgagatcactaaaatacaaaggct-cagatataagaaatcaattatgtttcattgt---------

upper sequence: GRMZM2G099255_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0103g00490.t01 (Vitis vinifera), 5'ss of exon 6
CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttttttttgtat-agtgacttttttttggcttccaataatcctctatcctccaaattcaat-tacttataacagttatggattctcatagttaacctcgaatattcttcaactacag
|||||| ||||||||||||||||||   || |||||||| || |||||| |||| ||||||| || ||  || |  |||||||| || |||||   || |  | |  ||| || | | ||   || | ||    | |  |  ||      ||| |  || |  ||||      | ||     | | |||||   | | | | |            
CTTTGAGGATCCTGGTCCACATGGAAATGGCAGATATTCAGAACATATGTTACCGGAAATTGAGATGAGTGACTTTAGAAAGGGCGCACAGgtataatctcatgtattatcagaggccttgcatttgttt---gtgagtcagtaga----aaacttgatgtgtttatgttcactttga----tgaaagtta--tttggacaata-----------

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|113702130|gb|EE679634.1|EE679634
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATACTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|78105512|gb|DV523930.1|DV523930
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|78090001|gb|DV518375.1|DV518375
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|76018436|gb|DT945606.1|DT945606
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|101398462|gb|EB821104.1|EB821104
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|86474172|gb|DY240542.1|DY240542
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|78093093|gb|DV521467.1|DV521467
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|86471048|gb|DY237418.1|DY237418
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|71774867|gb|DR972745.1|DR972745
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|78077573|gb|DV506007.1|DV506007
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|101388829|gb|EB816396.1|EB816396
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|148961000|gb|EE011700.2|EE011700
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|37388428|gb|CF631423.1|CF631423
EST:     GGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATACTCGCGGACACCCTT
genomic: GGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|71767366|gb|DR965303.1|DR965303
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|211278467|gb|FL480336.1|FL480336
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTGTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|149106921|gb|EE188822.2|EE188822
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|71442672|gb|DR823722.1|DR823722
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|86469460|gb|DY235830.1|DY235830
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|149082889|gb|EE172120.2|EE172120
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|50337694|gb|CO532820.1|CO532820
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|76912822|gb|DV164897.1|DV164897
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
EST: gi|148963210|gb|EE014187.2|EE014187
EST:     AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG                         TGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT
genomic: AGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttt ... tcaactacagTGGTTTACAGTGAAACGGCAGCATGCGATTCTTATTCTCGCGGACACCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAGgtgatatttttttttgtatagtgacttttttttggcttccaataatcctctatcctccaaattcaattacttataacagttatggattctcatagttaacctcgaatattcttcaactacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA