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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcaccgctatatacttcaataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA

Basic information

species Zea mays
transcript GRMZM2G059671_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
------------------------------------------------tggcaccgctatatacttca-ataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactct---attgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
                                                || |   |  |||| ||| | ||||||   |  ||| || |  | |  |||||| ||         | ||| | ||    ||| | || | ||||  | | ||||| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| 
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgac-tggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttc-gtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG

upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
----------tggcaccgctatatacttcaataaagctgacattggcctttcagttgaaat--tgaagcaatcgtcgtttaatactctattgtttgc-atcttct-atgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
              |      ||||||          |   | |    ||| | ||  |||     |    | ||  |||  || |  |   | ||  || || | || | |||||||| |||||||| ||||||||||| |||||||| || || || ||  | ||||| || || ||||||||  | |||||||| || || || ||||| 
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttttgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 12
--tggcaccgcta-tatacttcaataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
      || | |  |    || | ||    |||  |||   | |||  | ||| | |        |  ||| ||   | || || |   | |   || | |||||||| |||||||| ||||||||||| |||||||| || || || ||  | ||||| || || ||||||||  | |||||||| || || || ||||| 
aactctactgtttctgctttttagtatttttgaatttgtattgtca--taaaaataatctttgtattctttgattaaccat-gtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
tggcaccgctatatacttcaataaagctgacattggccttt---cagttgaaat---tgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
         | | |   | | |     |   ||   |||||   ||| | ||||   |      ||  || |||       | || |||   | |   |   |||||| || || ||||| ||||||||||| || |||||||| || || || || ||| | ||||| |||||||| |||||||||||||| ||||| ||||| 
------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|20802940|gb|BQ293990.1|BQ293990
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTTGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|67042437|gb|CO468692.1|CO468692
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GTAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|149096725|gb|EE182499.2|EE182499
EST:     GAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: GAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32836824|gb|CD976502.1|CD976502
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|71445939|gb|DR826989.1|DR826989
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         T
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacag-
EST: gi|71445939|gb|DR826989.1|DR826989
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         T
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacag-
EST: gi|26456437|gb|CA828020.1|CA828020
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|60358265|gb|DN225238.1|DN225238
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|60357002|gb|DN223975.1|DN223975
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32838830|gb|CD978511.1|CD978511
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|86471848|gb|DY238218.1|DY238218
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATACTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32836743|gb|CD976421.1|CD976421
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|71445940|gb|DR826990.1|DR826990
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|78544345|gb|DV621843.1|DV621843
EST:     CAA-GGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

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