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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctccatgtctgttctttagcgtttgtgttttaattcagcgtgcttcatgtttctttacatgagtttcctccaagtaaggttttttgttttgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGACGTGCTGCAACCTGGCAAGAACATGCTCGCCGCCGGATACTGCATGTACG

Basic information

species Zea mays
transcript GRMZM5G836250_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 5
---tctccatgtctgttctttagcgtttgtgttttaattcagcgtgcttcatgtttctttacatgagtttcctccaagtaaggttttttgttttgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGACGTGCTGCAACCTGGCAAGAACATGCTCGCCGCCGGATACTGCATGTACG
     || |  |   || | |        |  |   ||||     |    | |   ||||| |||  || |||  |    | ||| ||| | ||||||| |||||||||||||| ||||| ||||| || ||||| || || ||||| ||||||||| | || ||||| || |||||| | || || ||||||||||||||||
tagggtcaacttgaattgtcttcgaacaatactc-gattcgattcgtcagaaggaccttta-atggatt-cctgtactacatgttctttctcttgttttatagATCTTTGGGATCTACATGATCAAAGATAAGGAGAATGTGACTCTTGAGGACGTGTTACAGCCTGGAAAAAACATGGTTGCTGCTGGATACTGCATGTACG
















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:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTTACATCATCAAGGACAAGGGACAACG
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTT-ACATCATCAAGGACAAGG-ACAACG
EST: gi|149064613|gb|EE286484.2|EE286484
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|149085230|gb|EE174737.2|EE174737
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|149056940|gb|EE156494.2|EE156494
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|33466970|gb|CF244019.1|CF244019
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|50327741|gb|CO522867.1|CO522867
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|89759142|gb|DY688055.1|DY688055
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|211007786|gb|FL012051.1|FL012051
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACNAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|149088446|gb|EE177549.2|EE177549
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|149095912|gb|EE181574.2|EE181574
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|148983226|gb|EE029190.2|EE029190
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|71768089|gb|DR966026.1|DR966026
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|71770843|gb|DR968780.1|DR968780
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|32920842|gb|CF025654.1|CF025654
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGTGTCTCCATCGGAACG                         ATCTTTGGGATTTATATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|148932776|gb|EE285437.2|EE285437
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|71317308|gb|DR795339.1|DR795339
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|211005021|gb|FL012048.1|FL012048
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|94476279|gb|EB705237.1|EB705237
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|91055488|gb|EB165906.1|EB165906
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|91877810|gb|EB407767.1|EB407767
EST:     TCCCCTCGACGGCTCCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: TCCCCTCGACGGCTCC-TCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|32920947|gb|CF025759.1|CF025759
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTATATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|149040104|gb|EE046754.2|EE046754
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|76282215|gb|DV021783.1|DV021783
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACCAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|74244032|gb|DT651946.1|DT651946
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|93284535|gb|EB676799.1|EB676799
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTT
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTT
EST: gi|32921813|gb|CF026625.1|CF026625
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTATATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|32921310|gb|CF026122.1|CF026122
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTATATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|71438223|gb|DR819273.1|DR819273
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTTGGATTTGCATCATCAAGGACAAGGACAACGTCACTCTGGAAGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
EST: gi|71757120|gb|DR955057.1|DR955057
EST:     ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACG                         ATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC
genomic: ATCCCCTCGACGGCTCCTCCAACATCGACTGTGGCGTCTCCATCGGAACGgtatggacac ... tgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtttctttacatgagtttcctccaagtaaggttttttgttttgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGACGTGCTGCAACCTGGCAAGAACATGCTCGCCGCCGGATACTGCATGTACG
                                   ttttttgttttgtttt  CT-rich tract
                                   ttttttgttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctccatgtctgttctttagcgtttgtgttttaattcagcgtgcttcatgtttctttacatgagtttcctccaagtaaggttttttgttttgttttgtagATCTTTGGGATTTACATCATCAAGGACAAGGACAACGTCACTCTGGAGGACGTGCTGCAACCTGGCAAGAACATGCTCGCCGCCGGATACTGCATGTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC