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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaaccgcaattatgctttattgggaaggttgtctttgtccacacatactgtttctgagaactgtttcacttattttaatctatcttgctatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGTTCCTGCTTGGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCTACT

Basic information

species Zea mays
transcript GRMZM2G132465_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132465_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g16090.1 (Oryza sativa), 3'ss of exon 1
acaaaccgcaattatgctttattgggaaggttgtcttt-gtccacacatact----gtttctg-agaactgtttcacttattttaatctatcttgctatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGTTCCTGCTTGGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCTACT--------
      |     |||  ||| ||  |||  || | ||| || || ||| | |     ||| || ||| |  ||||||||||||| ||  | |||||||||| |||||||| |||||||||||||||||||||||||        ||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||| | |        
------catgtatatcattttttcagaaacttattttttgtacatacaaattttaactttttgcagacccatttcacttatttttattcaccttgctattttacagGATGCTTATAACTATTTTACTGTGGCCAGA--------TGATTCTACGTGTTCCTGCTTCGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCAAATCGATTACT
















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|32835390|gb|CD975068.1|CD975068
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|32833545|gb|CD973223.1|CD973223
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAANACATTACATGGGTCATTAG                         GATGATTATAACTATTTTATTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|37379216|gb|CF626343.1|CF626343
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|149000949|gb|EE038187.2|EE038187
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|33942233|gb|CF348833.1|CF348833
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|148981231|gb|EE027515.2|EE027515
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTTTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|166534138|gb|EG303333.1|EG303333
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTAC
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTAC
EST: gi|149099398|gb|EE185439.2|EE185439
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|211467707|gb|FL447950.1|FL447950
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|78120784|gb|DV539168.1|DV539168
EST:     ATGGGGGTGCTTTTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTTTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|148986760|gb|EE030554.2|EE030554
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTTTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|148959885|gb|EE153122.2|EE153122
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTTTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|78125185|gb|DV543569.1|DV543569
EST:     ATGGGGGTGCTTTTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTTCTGTGGCCAGAATGCCAGATGATTTTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|78079882|gb|DV508294.1|DV508294
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|91874933|gb|EB404890.1|EB404890
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|111433801|gb|EE298054.1|EE298054
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGANAGANTGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|89248594|gb|DY620380.1|DY620380
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|15208682|gb|BI430566.1|BI430566
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|211220368|gb|FL435935.1|FL435935
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|148929018|gb|EC874235.2|EC874235
EST:     GGGTGGTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: GGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|91052934|gb|EB163352.1|EB163352
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTTTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|166421293|gb|EG291038.1|EG291038
EST:     GGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: GGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|32834048|gb|CD973726.1|CD973726
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|89248593|gb|DY620379.1|DY620379
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCGGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|76010695|gb|DT937865.1|DT937865
EST:     ATGGGGGTGTTTTTTCAGGAGGCCCTGGAAGCCATTCCATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTTTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|32832990|gb|CD972668.1|CD972668
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|18650102|gb|BM498921.1|BM498921
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
EST: gi|148981520|gb|EE027706.2|EE027706
EST:     ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAG                         GATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT
genomic: ATGGGGGTGCTTCTTCAGGAGGCCCTGGAAGACATTACATGGGTCATTAGgtaagatttg ... tatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catactgtttctgagaactgtttcacttattttaatctatcttgctatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGTTCCTGCTTGGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCTACT
                             ttttaat  putative branch site (score: 3)
                                       tcttgct  putative PPT
                          ttattttaatctatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaaccgcaattatgctttattgggaaggttgtctttgtccacacatactgtttctgagaactgtttcacttattttaatctatcttgctatttgacagGATGATTATAACTATTTTACTGTGGCCAGAATGCCAGATGATTCTACATGTTCCTGCTTGGCACTTATAAACTTGCTGTTTTAAGCTGTTTCTGGCTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - tatgctt
- - - - - - - - - - - - - - - - - - - - ccacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttca