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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcaccgctatatacttcaataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG

Basic information

species Zea mays
transcript GRMZM2G059671_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
------------------------------------------------tggcaccgctatatacttca-ataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactct---attgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG
                                                || |   |  |||| ||| | ||||||   |  ||| || |  | |  |||||| ||         | ||| | ||    ||| | || | ||||  | | ||||| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||||||  
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgac-tggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttc-gtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG-

upper sequence: GRMZM2G059671_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
----------tggcaccgctatatacttcaataaagctgacattggcctttcagttgaaat--tgaagcaatcgtcgtttaatactctattgtttgc-atcttct-atgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG
              |      ||||||          |   | |    ||| | ||  |||     |    | ||  |||  || |  |   | ||  || || | || | |||||||| |||||||| ||||||||||| |||||||| || || || ||  | ||||| || || ||||||||  | |||||||| || || || |||||  
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttttgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG-

upper sequence: GRMZM2G059671_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 12
--tggcaccgcta-tatacttcaataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG
      || | |  |    || | ||    |||  |||   | |||  | ||| | |        |  ||| ||   | || || |   | |   || | |||||||| |||||||| ||||||||||| |||||||| || || || ||  | ||||| || || ||||||||  | |||||||| || || || |||||  
aactctactgtttctgctttttagtatttttgaatttgtattgtca--taaaaataatctttgtattctttgattaaccat-gtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG-

upper sequence: GRMZM2G059671_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
tggcaccgctatatacttcaataaagctgacattggccttt---cagttgaaat---tgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG
         | | |   | | |     |   ||   |||||   ||| | ||||   |      ||  || |||       | || |||   | |   |   |||||| || || ||||| ||||||||||| || |||||||| || || || || ||| | ||||| |||||||| |||||||||||||| ||||| |||||  
------tatttttttagtgattgttatttggatgcaccttttaccagctaaaataacttgttttattatcatttccgtgctttttttttttttttaaaacaaacagGCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAG-

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|32836824|gb|CD976502.1|CD976502
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32839244|gb|CD978925.1|CD978925
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32837172|gb|CD976850.1|CD976850
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32838830|gb|CD978511.1|CD978511
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32836743|gb|CD976421.1|CD976421
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaattgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG
                   gtttaat  putative branch site (score: 4)
                                       catcttct  putative PPT
                    tttaatactctatt  TA-rich tract