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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaatcagcccgcatcgcttgttttcactactctttcagttgttcgtttcaaatcgttggattcttgattgctatttgtttcttccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACCGGAGAAGGTTCTCAAGGCGGCCGGCGAGGTCGGCGCCTACGTCGACTGC

Basic information

species Zea mays
transcript GRMZM2G031825_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031825_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g21460.1 (Oryza sativa), 3'ss of exon 1
gtacgaatcagcccgcatcgcttgttttcactactctttcagttgttcgtttcaaatcgttggattcttgattgctatttgtttcttccgttc--gaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACCGGAGAAGGTTCTCAAGGCGGCCGGCGAGGTCGGCGCCTACGTCGACTGC
    | | |  || | |||  |  || ||| |  ||| |    |||||| |||   |   | |  ||||  ||| |  |  ||  ||  ||||  ||||||||||||||||||||||||||  ||| |||||||| ||||| ||||| ||||||||||| ||   ||||||||  |||||||||| |  | ||||||||
----gtaccctcctgaatccatccttgtcagttgtctgta---tgttcggttcttgtttcttggctctttcttgattatccttcgttttgttcttgaagAATCGTGGACGAGAGCACCAAGTCGGCGGCGGCCGTCGACCCCGTGGAGCCGGAGAAGGTGCTTGCGGCGGCCGCGGAGGTCGGCGTCCGCATCGACTGC

upper sequence: GRMZM2G031825_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G36610.1 (Glycine max), 3'ss of exon 1
gtacgaatcagcccgcatcgcttgttttcactactctttcagttgttcgtttcaaatcgttggattcttgattgctatttgtttcttccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACCGGAGAAGGTTCTCAAGGCGGCCGGCGAGGTCGGCGCCTACGTCGACTGC
                 |   | || |  |  | || |||| |   |  ||         | |||| |        | |  | |     |  || || ||||| ||||||||||| ||| | || ||||| || ||||| || |||||||||||||||||  | |  ||| ||  |  ||||  |    || | | |
----------------gtatgtagtatctaacattccttcattcaatttttct------cttgattttgatgaatgaatcatctgagtgg--cgcagGATCGTAGACGAGAGCACGAAGGAAGCCGCGGCGGTGGACCCGGTCGAACCGGAGAAGGTTCTTGAAGTTGCCAGCTCGCACGGCCTCACTCTCAAATTC
















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|211455844|gb|FL371246.1|FL371246
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211282892|gb|FL423639.1|FL423639
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211276907|gb|FL386582.1|FL386582
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211487768|gb|FL393005.1|FL393005
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211436196|gb|FL370281.1|FL370281
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211112220|gb|FL429165.1|FL429165
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211201689|gb|FL384215.1|FL384215
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211251969|gb|FL399229.1|FL399229
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211539553|gb|FL409993.1|FL409993
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|32910784|gb|CF015596.1|CF015596
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAAGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211133046|gb|FL407432.1|FL407432
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211445202|gb|FL371167.1|FL371167
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211451679|gb|FL376124.1|FL376124
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211520775|gb|FL373480.1|FL373480
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211262121|gb|FL420560.1|FL420560
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211143159|gb|FL403015.1|FL403015
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACC-TGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211265984|gb|FL369214.1|FL369214
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAAGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|32910981|gb|CF015793.1|CF015793
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAAGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211497290|gb|FL426479.1|FL426479
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211231771|gb|FL389681.1|FL389681
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211090884|gb|FL430012.1|FL430012
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211108385|gb|FL394493.1|FL394493
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211529760|gb|FL372707.1|FL372707
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACC
EST: gi|211464411|gb|FL419842.1|FL419842
EST:     CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTT                         AATCGTGGACGAGAGCACCAAGAAGGMAGCGGCCGTTTGACCCTGTGGAAC
genomic: CAGATGAAGATCATTCCGGTCCCTTGCCTGGATGACAACTATGCCTACTTgtacgaatca ... ccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCG-TTGACCCTGTGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcgtttcaaatcgttggattcttgattgctatttgtttcttccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACCGGAGAAGGTTCTCAAGGCGGCCGGCGAGGTCGGCGCCTACGTCGACTGC
                       tcttgat  putative branch site (score: 4)
                                   tttgtttcttccgttc  putative PPT
                                 tatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaatcagcccgcatcgcttgttttcactactctttcagttgttcgtttcaaatcgttggattcttgattgctatttgtttcttccgttcgaagAATCGTGGACGAGAGCACCAAGAAGGCAGCGGCCGTTGACCCTGTGGAACCGGAGAAGGTTCTCAAGGCGGCCGGCGAGGTCGGCGCCTACGTCGACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA