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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagactgaacttgttaattattgacctgcccgtttctctgatgaaatgtatgaatatgcgtcgcttttgtgtatccctaaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG

Basic information

species Zea mays
transcript GRMZM5G836250_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 4
--------------gtgagcagactgaacttgttaattattgacctg-----cccgtttctctgatgaaatgtatgaatatgcgtcgcttttgtgtatccctaaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG
               | || |    || ||   |  || ||||   |      | |||  |||| |       |  || || | |   |  ||    |   |    ||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
gtgcgtagcttcggatcagaaacgcgacctctctgcttcttgattcgagcaatctgttgttctgtttttcctgacaaa-atacatgcatggtgccggtttttt---ttacagGTATTGCGTGTGCTTTGATCCACTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG
















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|91877968|gb|EB407925.1|EB407925
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|149064613|gb|EE286484.2|EE286484
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|149085230|gb|EE174737.2|EE174737
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|149056940|gb|EE156494.2|EE156494
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|33466970|gb|CF244019.1|CF244019
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|78106830|gb|DV525248.1|DV525248
EST:     CCGAGGAGGACGAGGAAGNCA-CGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCCTCCA-CATCGACT
genomic: CCGAGGAGGACGAGGAAG-CAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCC-TCCAACATCGACT
EST: gi|148938587|gb|EC882914.2|EC882914
EST:     CCGAGGAGGACGAAGAAGCCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GGACTGCGTCTGC
genomic: CCGAGGAGGACGAGGAAGC-AACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGC
EST: gi|50327741|gb|CO522867.1|CO522867
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|89759142|gb|DY688055.1|DY688055
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|211007786|gb|FL012051.1|FL012051
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|149088446|gb|EE177549.2|EE177549
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|71314865|gb|DR794058.1|DR794058
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|149095912|gb|EE181574.2|EE181574
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|148983226|gb|EE029190.2|EE029190
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|71768089|gb|DR966026.1|DR966026
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|71770843|gb|DR968780.1|DR968780
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|148932776|gb|EE285437.2|EE285437
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|71317308|gb|DR795339.1|DR795339
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|211005021|gb|FL012048.1|FL012048
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|94476279|gb|EB705237.1|EB705237
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|91055488|gb|EB165906.1|EB165906
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|91877810|gb|EB407767.1|EB407767
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCCTCCAACATCGACTGTG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCC-TCCAACATCGACTGTG
EST: gi|149040104|gb|EE046754.2|EE046754
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|76282215|gb|DV021783.1|DV021783
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|74244032|gb|DT651946.1|DT651946
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|93284535|gb|EB676799.1|EB676799
EST:     TCCGAGGAGGATGAAGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|71438223|gb|DR819273.1|DR819273
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
EST: gi|71757120|gb|DR955057.1|DR955057
EST:     TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG                         GTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG
genomic: TCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGgtgagcagac ... aaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctgatgaaatgtatgaatatgcgtcgcttttgtgtatccctaaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG
                                         ccctaaa  putative branch site (score: 3)
          aaatgtatgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcagactgaacttgttaattattgacctgcccgtttctctgatgaaatgtatgaatatgcgtcgcttttgtgtatccctaaaattaaagGTACTGCGTCTGCTTTGATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC