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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttcagaagcttgccccccttttgttctcttcgatcagccaacaacattttttaccgagataaaaaaaactaaactgcatctgcatctgtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCT

Basic information

species Zea mays
transcript GRMZM2G099255_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
gtaagtgttcagaagcttgccccccttttgttctcttcgatcagccaacaacattttttaccgagataaaaaaaactaaactgcatctgcatctgtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCT
|||||   ||  ||     |     |  |||| |           ||      |||  | || ||           | |  |    | |    |||  | | ||||||||||||| ||||||||  | || ||||| ||||| ||||| || ||||| ||||| || |||||||| ||||  ||||||||||  ||||||||||
gtaagaactctcaaaaactcttaaatgatgttttt----------cagttgtgtttacttcccag-----------tgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT

upper sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0008g02630.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtgttcagaagcttgccccccttttgttct-----cttcgatcagccaacaacattttttaccgagataaaaaaaactaaactgcatctgcatctgtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCT
|| ||       ||  |||  | | ||||    |     |||   | |  |      ||| ||| |     |  || |       |  |  ||||     ||     ||||| | ||||| ||||||||  | |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||  ||||||| |   |||   || |
gtcagcacattaaactttgtactctttttcccataaaaccttgtgttaaaccctcctattatttccttgtttccaacatttcttcccactgctgc-----tgctttcagATGATCGATCCTACTGGAATTGCAAACTGGTCTGTGACACATGTAGATTGGTCAGAAGGAAAGTGGCATCCAAAAGCATACAGGGGTCAAGACGTCAGTT
















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:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|78105512|gb|DV523930.1|DV523930
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|78090001|gb|DV518375.1|DV518375
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|76018436|gb|DT945606.1|DT945606
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|101398462|gb|EB821104.1|EB821104
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|86474172|gb|DY240542.1|DY240542
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|89252603|gb|DY624389.1|DY624389
EST:     CATAACTGTTATTCAGACGAGCACTCCTTGCCACCCCTCTTTAAC                         ATGGTTGATCGGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: CATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|78093093|gb|DV521467.1|DV521467
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|211482405|gb|FK951270.1|FK951270
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|86471048|gb|DY237418.1|DY237418
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|71774867|gb|DR972745.1|DR972745
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|101399747|gb|EB821720.1|EB821720
EST:     AATGGCATAAGTGCTATTCAGACGAGCGCTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|78077573|gb|DV506007.1|DV506007
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|101388829|gb|EB816396.1|EB816396
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|148961000|gb|EE011700.2|EE011700
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|37388428|gb|CF631423.1|CF631423
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|71767366|gb|DR965303.1|DR965303
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|211278467|gb|FL480336.1|FL480336
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCG
EST: gi|149106921|gb|EE188822.2|EE188822
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|211485273|gb|FK951273.1|FK951273
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|71442672|gb|DR823722.1|DR823722
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|37394285|gb|CF634415.1|CF634415
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGTCTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|86469460|gb|DY235830.1|DY235830
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|149082889|gb|EE172120.2|EE172120
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|50337694|gb|CO532820.1|CO532820
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|76912822|gb|DV164897.1|DV164897
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
EST: gi|148963210|gb|EE014187.2|EE014187
EST:     AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAAC                         ATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG
genomic: AATGGCATAACTGCTATTCAGACGAGCACTACTTGCCAACCCTCTTTAACgtaagtgttc ... gtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacattttttaccgagataaaaaaaactaaactgcatctgcatctgtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCT
                        aactaaa  putative branch site (score: 2)
              agataaaaaaaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttcagaagcttgccccccttttgttctcttcgatcagccaacaacattttttaccgagataaaaaaaactaaactgcatctgcatctgtggccgaagATGGTTGATCCGACTGGAATCTCGAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT