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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaaatttattgccctcgagctctacttgttacccagttcatgttcatagaaacacttctaggtggaactctgattattcctcgtacaattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGAGTATCTGTCA

Basic information

species Zea mays
transcript GRMZM2G147614_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147614_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 3
gtaataaaatttattgccctcgagctctacttgttacccagttcatgttcatagaaacactt--ctaggtggaactctgattattcc--tcgtacaattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGAGTATCTGTCA
                     |   || |    || |||  |   |  |||| ||| |||||    |     |||| | ||| ||||  ||   ||  ||| |||||||| |||||| ||| |||||| |||||||| || | ||| |||||||||||||||||||
---------------------gtattcaatgcctt-ccctttagctcctcatggaagcactttgtcaatcataactgttattgttccattcactcatgtttacagGCAGAACTGGTTCACCGAGTTGAAAAGCATCTCATGAATATTATGCATGGAGTATCTGTCA
















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|86472598|gb|DY238968.1|DY238968
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTA
EST: gi|93013166|gb|EB638686.1|EB638686
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|211034641|gb|FL277424.1|FL277424
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACCTGAAC                         GCAGAGCTGGTTAACC
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACC
EST: gi|89106294|gb|DY576511.1|DY576511
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|211037077|gb|FL277427.1|FL277427
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|17921703|gb|BM259354.1|BM259354
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|86474214|gb|DY240584.1|DY240584
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|74238971|gb|DT646885.1|DT646885
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|60345606|gb|DN212579.1|DN212579
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|22489535|gb|BU049458.1|BU049458
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|32865677|gb|CF005359.1|CF005359
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCAT
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCAT
EST: gi|17921875|gb|BM259526.1|BM259526
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|16927590|gb|BM080659.1|BM080659
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|22543221|gb|BU093659.1|BU093659
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGCTAACCAAGTTGAGAAGCATCTTATCAGCATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|40334273|gb|CK368343.1|CK368343
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|9254485|gb|BE344953.1|BE344953
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|33771015|gb|CF273309.1|CF273309
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACCTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|89106285|gb|DY576502.1|DY576502
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|21331342|gb|BQ486723.1|BQ486723
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|211037078|gb|FL277428.1|FL277428
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|211037076|gb|FL277426.1|FL277426
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|21331390|gb|BQ486771.1|BQ486771
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAGCCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|17921548|gb|BM259199.1|BM259199
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|211240386|gb|FL373755.1|FL373755
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACCTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|74235859|gb|DT643773.1|DT643773
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|211183920|gb|FL459369.1|FL459369
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|74235860|gb|DT643774.1|DT643774
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|211037079|gb|FL277429.1|FL277429
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACCTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|86472597|gb|DY238967.1|DY238967
EST:     CAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
EST: gi|78544005|gb|DV621503.1|DV621503
EST:     CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAAC                         GCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA
genomic: CAATGAGGGATGCACGCAGGCGACGTTTCCGCAGAGAACCAGACTTGAACgtaataaaat ... aattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcatagaaacacttctaggtggaactctgattattcctcgtacaattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGAGTATCTGTCA
                          ctctgat  putative branch site (score: 4)
                                          tacaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaaatttattgccctcgagctctacttgttacccagttcatgttcatagaaacacttctaggtggaactctgattattcctcgtacaattttgcagGCAGAGCTGGTTAACCAAGTTGAGAAGCATCTTATCAGTATCATGCATGGAGTATCTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA