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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagctctctgcggccttttacctcttacttgttgccttttaattaacctataacctcatcacaagtcgtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTCGACGCCGTACGTGGTGACGCTCTTCAGCTGCATGCTGTGGATCTTGTAC

Basic information

species Zea mays
transcript GRMZM2G168365_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168365_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g30910.1 (Oryza sativa), 3'ss of exon 2
-----gtaagtagctctctgcggcct-tttacctcttacttgttgccttttaattaacctataacctcatcacaagt---------cgtttc---tgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTCGACGCCGTACGTGGTGACGCTCTTCAGCTGCATGCTGTGGATCTTGTAC
     | ||| | ||       ||   |||     | |||  ||         || | | ||||| | | |    ||         |||||    |||||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |  |||
cagacgaaagaaactgctgttagctagtttgttgataactaattattagcaggttgaacaataacttaaccgtgtgtgcatgcgtgcgtttggcgtgcagGCCGACGTTCTACCGGGTGTACCGGAAGAAGTCGACGGAGGGGTTCCAGTCGACGCCGTACGTGGTGACGCTCTTCAGCTGCATGCTGTGGATGTACTAC
















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|211255179|gb|FL327773.1|FL327773
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|149101593|gb|EE187720.2|EE187720
EST:     GGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: GGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211098083|gb|FL308906.1|FL308906
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211059310|gb|FL364338.1|FL364338
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|40335419|gb|CK369489.1|CK369489
EST:     GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211515173|gb|FL354453.1|FL354453
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|148995998|gb|EE035249.2|EE035249
EST:     ACATAGTCTCACTGATGGTGTTTCTTTCACCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: ACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211500953|gb|FL349221.1|FL349221
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211359391|gb|FL326979.1|FL326979
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211020734|gb|FL318484.1|FL318484
EST:     AACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGDNGGGTTCCAGTC
genomic: AACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211517549|gb|FL354938.1|FL354938
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211378521|gb|FL350955.1|FL350955
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211289713|gb|FL361715.1|FL361715
EST:     AACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211018146|gb|FL327158.1|FL327158
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211512468|gb|FL332428.1|FL332428
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211019027|gb|FL359016.1|FL359016
EST:     GTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|149100156|gb|EE186212.2|EE186212
EST:     GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211383054|gb|FL320862.1|FL320862
EST:     GTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211342622|gb|FL344344.1|FL344344
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211050329|gb|FL359890.1|FL359890
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211088349|gb|FL312042.1|FL312042
EST:     GTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|78088794|gb|DV517187.1|DV517187
EST:     GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: GTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211467660|gb|FL334998.1|FL334998
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGASGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211224744|gb|FL338382.1|FL338382
EST:     AACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211160992|gb|FL363058.1|FL363058
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211427339|gb|FL330523.1|FL330523
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211422113|gb|FL330481.1|FL330481
EST:     AACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|148930741|gb|EC873035.2|EC873035
EST:     CATAGTCTCACTGATGGTGTTTCTTTCACCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: CATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211349655|gb|FL335831.1|FL335831
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCSGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211534511|gb|FL328894.1|FL328894
EST:     CATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: CATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211531452|gb|FL327592.1|FL327592
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211159370|gb|FL361290.1|FL361290
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
EST: gi|211495794|gb|FL368176.1|FL368176
EST:     AGGTAACATAGTCTCACTGATGGTGTTTCTTTCGCCGCT                         GCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC
genomic: AGGTAACATAGTCTCACTGATGGTGTTTCTTTCACCGCTgtaagtagct ... gtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttacttgttgccttttaattaacctataacctcatcacaagtcgtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTCGACGCCGTACGTGGTGACGCTCTTCAGCTGCATGCTGTGGATCTTGTAC
                                           tcgtttct  CT-rich tract
              ttttaattaacctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagctctctgcggccttttacctcttacttgttgccttttaattaacctataacctcatcacaagtcgtttctgcagGCCGACGTTCTACCGCGTGTACCGCAACAAGTCGACGGAGGGGTTCCAGTCGACGCCGTACGTGGTGACGCTCTTCAGCTGCATGCTGTGGATCTTGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG