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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccctgcacatttatatcttctgtgtgtttctcgcggtggttctgttcaatgagcacctatttaatcaaatttgcattcacaaatataagtgaatggtgactacaaataacgctaacagcagatagcctaagaaatcttttcaatgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGATGTGTTTGCATCTGCAACTGAGAGAGACATCTACACT

Basic information

species Zea mays
transcript GRMZM2G074386_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074386_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g32800.2 (Oryza sativa), 3'ss of exon 5
---------gtaagccctgcacatttat-atcttctgtgtgtttctcgcggtggttctgttcaatgagcacctatttaatcaaatttgca--ttca-----caaatataagtgaatggt-gactacaaataacgctaacagcagatagcctaagaaatcttttcaatgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGATGTGTTTGCATCTGCAACTGAGAGAGACATCTACACT
           |||   | |   ||| | | ||    ||||  |   |   || |  |||    ||| || ||  || ||   |  ||||  || |     ||   | || | | || |  ||| |  ||     || |  ||  ||| |  |  ||| |||   |||    |||||||| |||||||| ||||||||| |||||||  ||||| |||| ||||||||||||||||| ||||||||||| ||||||||||||
gtaaggcactgaagttttactagtttgttacctggcatgtgcattatg-attgatcatgtcatgtgatcatctggttgatttgacatgcaagtttatgtgccacccagaaataagtgctcaactgctgatttgaatagctccac-tagtcctaagaatatttctgatgcatgcagGATGCCGTCACACCTTTGTCGGAGACAGAGGCGGTCGATTTAGTGAAGGATGTGTTTGCATCGGCAACTGAGAGGGACATCTACACT
















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|149016788|gb|EE154282.2|EE154282
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|45847129|gb|CN071072.1|CN071072
EST:     TCCTGGACAATCAACTAAAATCCCCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|71428371|gb|DR809421.1|DR809421
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|30087522|gb|CB885728.1|CB885728
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|31362426|gb|CD446783.1|CD446783
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|32938641|gb|CF043460.1|CF043460
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAAG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|149088717|gb|EE177839.2|EE177839
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTTTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|78106986|gb|DV525404.1|DV525404
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|17930931|gb|BM267891.1|BM267891
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|32938447|gb|CF043266.1|CF043266
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAAG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|7135769|gb|AW498256.1|AW498256
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|67031178|gb|CO459927.1|CO459927
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|74239718|gb|DT647632.1|DT647632
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|12968327|gb|BG265273.1|BG265273
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|24769350|gb|CA404479.1|CA404479
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|149111500|gb|EE295003.2|EE295003
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|32847010|gb|CD986691.1|CD986691
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAAG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|16926492|gb|BM079560.1|BM079560
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|60352481|gb|DN219454.1|DN219454
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|61118932|gb|DN559893.1|DN559893
EST:     TCCTGGACAATCAGCTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|14717546|gb|BI245196.1|BI245196
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|14243859|gb|BG841581.2|BG841581
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|17932205|gb|BM269165.1|BM269165
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|76013087|gb|DT940257.1|DT940257
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|40302852|gb|CK347239.1|CK347239
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|74240043|gb|DT647957.1|DT647957
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|60340468|gb|DN207441.1|DN207441
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAAG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|78109496|gb|DV527912.1|DV527912
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|14243256|gb|BG840908.2|BG840908
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactacaaataacgctaacagcagatagcctaagaaatcttttcaatgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGATGTGTTTGCATCTGCAACTGAGAGAGACATCTACACT
            cgctaac  putative branch site (score: 2)
                                  aaatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccctgcacatttatatcttctgtgtgtttctcgcggtggttctgttcaatgagcacctatttaatcaaatttgcattcacaaatataagtgaatggtgactacaaataacgctaacagcagatagcctaagaaatcttttcaatgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGATGTGTTTGCATCTGCAACTGAGAGAGACATCTACACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG