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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgctcaacattgcagcaagcaattcttggcatttcccttgccagaacttcattgttttaaggtgttttctcaatgttgataattctcatacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGTCTACAATTGTGAGAG

Basic information

species Zea mays
transcript GRMZM2G116919_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116919_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 4
agttgctcaacattgcagcaagcaattcttggcatttcccttgccagaacttcat-tgttttaaggtgt----tttctcaatgttgataattctcatacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGTCTACAATTGTGAGAG
      |  | | ||    ||  || |       | |   || |  |  | |||| || || |||  ||    ||||||| |||  || || ||  | |||||||||||| ||||| ||||||||||||||||||| ||   |||| |  |||||||| ||||||||||| |||||||||| |||||| ||||||||
----agtataaactgtgaaaaagaagtgcaaatttgttattt-cttgttcctcatatggttgaagaggtcttgtttctcactgtgaattatacttgtgcttgcagATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG
















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|37421879|gb|CF648643.1|CF648643
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|76917612|gb|DV166918.1|DV166918
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|50332246|gb|CO527372.1|CO527372
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|78544504|gb|DV622002.1|DV622002
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|88756479|gb|DY540620.1|DY540620
EST:     CATTCTCACTGGGGTTCTGTCCTTCAGG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|34391285|gb|CF384513.1|CF384513
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATAAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|78123531|gb|DV541915.1|DV541915
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|71420480|gb|DR805114.1|DR805114
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|67022830|gb|CO451579.1|CO451579
EST:     CATTCTCACTGGGCTTCTGTCTTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATAAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|31364477|gb|CD448832.1|CD448832
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATAAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|4804485|gb|AI665355.2|AI665355
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|37382371|gb|CF628128.1|CF628128
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATAAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|5343079|gb|AI795489.1|AI795489
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|71756603|gb|DR954540.1|DR954540
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|8103224|gb|AW927877.1|AW927877
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATAAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|60346203|gb|DN213176.1|DN213176
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATAAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|78024877|gb|DV493264.1|DV493264
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|71320224|gb|DR796871.1|DR796871
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|9742575|gb|BE518723.1|BE518723
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|60341447|gb|DN208420.1|DN208420
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
EST: gi|16920917|gb|BM074893.1|BM074893
EST:     CATTCTCACTGGGCTTCTGTCCTTCATG                         ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG
genomic: CATTCTCACTGGGCTTCTGTCCTTCATGgtaagttgtt ... atacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacttcattgttttaaggtgttttctcaatgttgataattctcatacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGTCTACAATTGTGAGAG
                               tgttgat  putative branch site (score: 4)
                                        ttctcat  putative PPT
        attgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgctcaacattgcagcaagcaattcttggcatttcccttgccagaacttcattgttttaaggtgttttctcaatgttgataattctcatacttgcagATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGTCTACAATTGTGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG