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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaattaacctcaaatctttgtacataatctcctttgtcctgtaccttctattgtcagtagctgctgcctgtagctcttaaagctcatcttgca...

Basic information

species Zea mays
transcript GRMZM5G852968_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G852968_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 5'ss of exon 8
GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaattaacctcaaatctttgtacataatctcctttgtcctgtaccttctattgtcagtagctgctgcc-tgtagctc----ttaaagctcatcttgca----------------
||||||| ||||||||||| ||||| ||||||||||||||||| ||||| || || || ||||||||||||||||| |||||||||||  |||||||| ||| ||| |   | | |  ||  |   | | ||    |  |      | | | |||    ||||  |     ||  |  ||||   |||                
GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAGgtatgataaattaacatcatatcctgaaatacagcctgttgattgccgtgttcttaaaccaatgaacccgctattgtgtaattgtgtattgtatttcattacgcaacattccgttttgcag

upper sequence: GRMZM5G852968_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G36990.1 (Glycine max), 5'ss of exon 8
GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaattaacctcaaatctttgtacataatctcctttgtcctgtaccttctattgtcagtagct-gctgcctgtagctcttaaagctcatcttgca---------
| ||||| |||| ||  ||| |||| |||||||||||| |||| ||||| ||||| ||||| ||||| ||||| || || ||||||       ||   |  || |  ||  ||  ||          | ||        |      ||   | | | | | || ||    ||| | ||||||           
GGTCTGTAAATGGAGGGAACAGTGCTGAGCTAGCAAAGCAAGAAGATATTGATGGATTTCTCGTTGGAGGTGCTTCATTAAAGgtaca-tggtttcttcaaaatttgtttgaccaaagtgagcaaagcatgagttaaggaactcaggttattagttacatata-cttgacaagttgatcttgttgaggtgcag

upper sequence: GRMZM5G852968_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G20930.1 (Glycine max), 5'ss of exon 8
GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatg-gcaaattaacctcaaa---tctttgtacataatctcctttgtcctgtaccttcta--ttgtcagtagctgctgcctgtagctct-taaagctcatcttgca---
| ||||| ||||||  |||| |||| ||||| |||||| |||| ||||| ||||| ||||||||||||||||| || || ||||||    ||   |    |||||   ||||||  || |      |   ||||  |  || ||  |   |   |     ||  | |   | | |  |  |  |  || |   
GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtacacacacggtttattcaaagtttctttgaccagatgtgtttcattcctagagtttgtaaatgaactcgaatgattgtttattaatgtgttgattttttgctgtacag

upper sequence: GRMZM5G852968_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G06740.1 (Glycine max), 5'ss of exon 8
GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaattaacctcaaat-ctttgtacataatctcctttgt-cctgtaccttcta--ttgtcagtagctgctgcctgtagctct-taaagctcatcttgca---
| ||||| |||||   |||| |||| ||||| || ||| |||| ||||| ||||| ||||||||||||||||| || || ||||||   | | |||  | ||| | |||||   | ||| | |||  | |||  |  || ||  |   ||  |     ||  |   | | | |  |  |  |  || |   
GGTCTGTAAATGCGAGCAACAGTGCTGAGCTCGCGAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAGgtaca-cgatttattcacaacttctttgactagaatgtgcttcattcctagagtttgtaaatgaacacgaatgaatgtttactgatgtattgattttttgctgtacag

upper sequence: GRMZM5G852968_T03 (Zea mays), 5'ss of exon 8
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 5'ss of exon 7
GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaattaacctcaaatctttgtacataatctcctttgtcctgtaccttctattgtcagtagctgctgcctgtagctcttaaagctcatcttgca
||||||| |||| || |||| |||||||||| || ||  |||| || || ||||| ||||||||||||||||||||||||||||||    || | ||  | | | |||| |  |||        |||  |  |         || |  ||| |||  |  |  |  |||  |    ||| |  
GTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAGgtaa---aagtaaagtttagacctttatggata--------tgttgttgatgaatagaagtaa--agcagctcacactcacctttattgtgactctag--

upper sequence: GRMZM5G852968_T03 (Zea mays), 5'ss of exon 8
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 5'ss of exon 8
GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaattaacctcaaatctttgtacataat--ctcctttgtcctgtaccttctattgtcagtagctgctgcctgtagctcttaaagctcatcttgca----
|||| |||||||    ||| ||| ||||||| || ||  |||||||||| ||||| ||||||||||| ||||| ||||| |||||||   |  || ||       |||   |  ||||  ||  |||| |   ||      ||    |  | ||  ||     |    |  ||    || ||       
GTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAGgtat---atttttactgttgggcttaaaaattaataactagtttgac---taaaagtaataaagaaaaacttatgataaaaaacttacaaaaaaattttaggagct

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|13126489|gb|BG317059.1|BG317059
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|60395080|gb|DN227949.1|DN227949
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|211221685|gb|FL287481.1|FL287481
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|86469699|gb|DY236069.1|DY236069
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|37381263|gb|CF627507.1|CF627507
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|166423749|gb|EG285216.1|EG285216
EST:     CCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|32848590|gb|CD988271.1|CD988271
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGC
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGC
EST: gi|211231463|gb|FL476105.1|FL476105
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|60344413|gb|DN211386.1|DN211386
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|78089319|gb|DV517693.1|DV517693
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|32848878|gb|CD988559.1|CD988559
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|78089191|gb|DV517575.1|DV517575
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|32843435|gb|CD983116.1|CD983116
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|37377574|gb|CF625404.1|CF625404
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|45567946|gb|CK985826.1|CK985826
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|60400606|gb|DN233413.1|DN233413
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|32849488|gb|CD989169.1|CD989169
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|71758305|gb|DR956242.1|DR956242
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|33099809|gb|CF059769.1|CF059769
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
EST: gi|32926274|gb|CF031086.1|CF031086
EST:     CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG                         GCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA
genomic: CAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaa ... gttttggcagGCCCCGGACTTCGCCACCATTATCAACTCAGTGACCGCCAAGAAAGTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAGgtatggcaaattaacctcaaatctttgtacataatctcctttgtcctgtaccttctattgtcagtagctgctgcctgtagctcttaaagctcatcttgca

- - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG