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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaccagccatgtattctcttatgttatttttctagtttcaaatatgaatatgtttctatgtaacatcctcctcctaacatgaccgcgttcctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTTGTGTATTGCTTGTACCATGTAATGCATGCCAGTCCATATACACGGGTAC

Basic information

species Zea mays
transcript GRMZM2G362088_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 7
ttaccagccatgtattctcttatgttatttttctagtttcaaatatgaatatgtttctatgt-aacatcctcctcctaacatgaccgcgttcctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTTGTGTATTGCTTGTACCATGTAATGCATGCCAGTCCATA-TACACGGGTAC---
||   | ||   |||  |   || || ||  |  | |    |    | | | |   || ||| ||| || ||||| |||| ||| |  ||||||   |||||||||||| ||||||||||| ||||||||||| || ||| |     |||  |||| ||| ||| |   || ||  ||| | ||    || |   |  |||    
tttttatcctcttatgtttaaatctt-ttgctacactacatagctgggaaaagaaactttgtgaacgtcgtcctcataacttgatcatgttccttgtacagGAAATTGCGAAGAGGTTGCCCAGGCCAACGGCGTCTTGATAATTAGCTTCGGTGT-TTG-TTGAA--GTGGAACACATACAAGCTGGTAATGTGCATGTAACAT
















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|211392787|gb|FL282754.1|FL282754
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|60341032|gb|DN208005.1|DN208005
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|37401257|gb|CF637991.1|CF637991
EST:     TCATTGAGTCGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|60347047|gb|DN214020.1|DN214020
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|32854499|gb|CD994180.1|CD994180
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAGTATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|50330000|gb|CO525126.1|CO525126
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCACCTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|74243754|gb|DT651668.1|DT651668
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|149074254|gb|EE162627.2|EE162627
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAAGTTGCCTAAGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|149078434|gb|EE167210.2|EE167210
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|74243753|gb|DT651667.1|DT651667
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|149094891|gb|EE180469.2|EE180469
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|211222474|gb|FL437630.1|FL437630
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|148970442|gb|EE021292.2|EE021292
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GACATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|148958503|gb|EC904742.2|EC904742
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAAACG-CATCGTGACAGAACACTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAA-CGGCATCGTGACAGAACACTTT
EST: gi|78091625|gb|DV519999.1|DV519999
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|78084796|gb|DV513189.1|DV513189
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|40336982|gb|CK371052.1|CK371052
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTTGCAA-GAGGTTGCCTAGGCCAACGGC
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATT-GCAAAGAGGTTGCCTAGGCCAACGGC
EST: gi|149094892|gb|EE180470.2|EE180470
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|32856098|gb|CD995779.1|CD995779
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCATCGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|32940145|gb|CF044964.1|CF044964
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|211392788|gb|FL282755.1|FL282755
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|18179553|gb|BM380763.1|BM380763
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|67021249|gb|CO449998.1|CO449998
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|78021899|gb|DV490286.1|DV490286
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTGT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|110201225|gb|EC883122.1|EC883122
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGCCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
EST: gi|149014736|gb|EE044417.2|EE044417
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCNAAGAGGTTGCCTAG
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAG
EST: gi|13381875|gb|BG458550.1|BG458550
EST:     TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG                         GAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT
genomic: TCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttg ... cctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatatgtttctatgtaacatcctcctcctaacatgaccgcgttcctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTTGTGTATTGCTTGTACCATGTAATGCATGCCAGTCCATATACACGGGTAC
                           tcctaac  putative branch site (score: 1)
                                         cgttcct  putative PPT
        tttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaccagccatgtattctcttatgttatttttctagtttcaaatatgaatatgtttctatgtaacatcctcctcctaacatgaccgcgttcctgtaacagGAAATTGCAAAGAGGTTGCCTAGGCCAACGGCATCGTGACAGAACACTTTTGTGTATTGCTTGTACCATGTAATGCATGCCAGTCCATATACACGGGTAC

-taccagc
- - - - catgtat
- - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgacc