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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatactaaccttatttatattttgaatattaggagtccaattagtccattttgttagcaactcattgtcaaagtgccttttgacatttctagtccggtacactgacagttgttgcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCAGAAATATGCTCACCAA

Basic information

species Zea mays
transcript GRMZM2G107731_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107731_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g17930.2 (Oryza sativa), 3'ss of exon 6
---------------------------------------------------------gtaagatactaaccttatttatattttgaatattaggagtccaattagtccattttgttagcaactcattgtcaaagtgccttttgacatttctagtccggtac--actgacagttgttgcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCAGAAATATGCTCACCAA
                                                          |  | | | ||| | |||    || | |  | || |              | | |  ||    || || ||  || | ||||   | ||||    | || ||   | ||  || |  ||  |||||||| ||||||||||||| ||||||||||| ||||||||||| || || ||||||||||||||||| || 
gtaagatactgaagttatgcctatgttctgtattaagagtttcttcaagtggattgaatttgttgccaacatcattgcacttctaatgactacgttcattgcagtcttaatctactacaggcttat-gtttaatttcctt---agattttgttttcgataatgattggtagcttatg--tttgtagGCTGAGAAGTAAACTCAAAGACCTTGCAGATCAATATAATATCACACAGCAGAAATATGCTCATCAG
















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|149081200|gb|EE170309.2|EE170309
EST:     CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC                         GTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTAC
genomic: CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATACgtaagatact ... gcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTAC
EST: gi|149027108|gb|EE046399.2|EE046399
EST:     CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC                         GTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
genomic: CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATACgtaagatact ... gcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
EST: gi|37394977|gb|CF634768.1|CF634768
EST:     AGAGAACCATTAC                         GTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGC
genomic: AGAGAA-CAATACgtaagatact ... gcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGC
EST: gi|213169996|gb|FM189145.1|FM189145
EST:     CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC                         GTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
genomic: CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATACgtaagatact ... gcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
EST: gi|32931571|gb|CF036383.1|CF036383
EST:     CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC                         GTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
genomic: CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATACgtaagatact ... gcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
EST: gi|31354731|gb|CD439088.1|CD439088
EST:     CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC                         GTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
genomic: CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATACgtaagatact ... gcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
EST: gi|60358220|gb|DN225193.1|DN225193
EST:     CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC                         GTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA
genomic: CTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATACgtaagatact ... gcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagtgccttttgacatttctagtccggtacactgacagttgttgcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCAGAAATATGCTCACCAA
                               cactgac  putative branch site (score: 2)
                                           ttgctttt  putative PPT
                atttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatactaaccttatttatattttgaatattaggagtccaattagtccattttgttagcaactcattgtcaaagtgccttttgacatttctagtccggtacactgacagttgttgcttttgtagGTTGAGAAGTAAACTGAAAGACCTTGCTGATCAATATAACATTACTCAGCAGAAATATGCTCACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT