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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacccccccccccccccccccctcgcctcccgtgtcgtccctccttctcgccccggatctcgaattccttacagtttcgccccctgcccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATTGCCAGCGACCGGCGGCTCGGCGTGCAGCTTCAGACCATCG

Basic information

species Zea mays
transcript GRMZM2G045371_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045371_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g43570.1 (Oryza sativa), 3'ss of exon 2
gtgagtacccccccccccccccccccctcgcctcccgtgtcgtccctccttctcgccccggatctcgaattccttacagtttcgccccctgcccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATTGCCAGCGACCGGCGGCTCGGCGTGCAGCTTCAGACCATCG
|||||| |||||| || |||| | |||| |||  ||| | || ||  ||       | |||||||  |||||             ||| ||||  | ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||| |||||| |||
gtgagtgccccccgccgccccgctccctggccggccgggccgcccgccc-------cacggatctt-aattct------------cccatgcc--tcgcagATCTTCGAGTACAATGGTTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGGCGGCTCGGGGTGCAGCTGCAGACCGTCG
















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|211320125|gb|FL100656.1|FL100656
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211320131|gb|FL100662.1|FL100662
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|76018879|gb|DT946049.1|DT946049
EST:     CCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211320126|gb|FL100657.1|FL100657
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|32908095|gb|CF012908.1|CF012908
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|15214985|gb|BI431121.1|BI431121
EST:     TCCGGCTATGTCA                         ATCTTCGAGTACAACGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|32914687|gb|CF019499.1|CF019499
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGTAG-TCTGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|78106724|gb|DV525142.1|DV525142
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|76923710|gb|DV169620.1|DV169620
EST:     CTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211320129|gb|FL100660.1|FL100660
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211320128|gb|FL100659.1|FL100659
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|32913371|gb|CF018183.1|CF018183
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|60398455|gb|DN231271.1|DN231271
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|32858096|gb|CD997777.1|CD997777
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|71438351|gb|DR819401.1|DR819401
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211320127|gb|FL100658.1|FL100658
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|76284605|gb|DV024173.1|DV024173
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|78091664|gb|DV520038.1|DV520038
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|50337097|gb|CO532223.1|CO532223
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211320444|gb|FL345949.1|FL345949
EST:     GCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAACGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: GCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|78086605|gb|DV514998.1|DV514998
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|31361651|gb|CD446008.1|CD446008
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|71774247|gb|DR972125.1|DR972125
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|116827042|gb|EC870897.1|EC870897
EST:     GCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTAC-ACGGGTCCGCTGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: GCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|32850853|gb|CD990534.1|CD990534
EST:     CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: CTTCTCCGCGAAATAGCCGTCGCCGCACTGCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211275645|gb|FL309928.1|FL309928
EST:     GCCGCAGCTCCGGCTATGTCA                         ATCTTCGAGTACAACGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: GCCGCAGCTCCGGCTATGTCAgtgagtaccc ... cccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttctcgccccggatctcgaattccttacagtttcgccccctgcccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATTGCCAGCGACCGGCGGCTCGGCGTGCAGCTTCAGACCATCG
                        tccttac  putative branch site (score: 2)
                                 tttcgccccctgccc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacccccccccccccccccccctcgcctcccgtgtcgtccctccttctcgccccggatctcgaattccttacagtttcgccccctgcccattgcagATCTTCGAGTACAATGGGTCCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATTGCCAGCGACCGGCGGCTCGGCGTGCAGCTTCAGACCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT