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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagttattactgcctaccgcttcattgatctctcttcttgacaccttcagttggttctgaactgtaaaagctctgcatcctgcagCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGTGAAGCAGCACGCGGTGCAGCGAGGGCAGCGTTTTGATGAAAACCGTATA

Basic information

species Zea mays
transcript GRMZM2G011078_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011078_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g38590.2 (Oryza sativa), 3'ss of exon 12
-----------------------gtgaagttattactgcctaccgcttcattgatctct--cttcttgacaccttc--------agttggttctgaactgtaaaagctctgcatcctgca-----gCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGTGAAGCAGCACGCGGTGCAGCGAGGGCAGCGTTTTGATGAAAACCGTATA-
                       ||    |  |   |   | | | | | |  || |||   | |||  |   ||         | ||  |       ||| |   || |||  ||||||     ||| || || || |||||||| || ||||||||||| || ||||||| ||| || || |||||| | ||||||||||| ||||||||||||  |  |||   
gtgggttattcaggtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGAT-GTACGT

upper sequence: GRMZM2G011078_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 12
----------gtgaagttattactgcctaccgcttcattgatctctc--ttcttgacaccttc--------agttggttctgaactgtaaaagctctgcatcctgca-----gCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGTGAAGCAGCACGCGGTGCAGCGAGGGCAGCGTTTTGATGAAAACCGTATA-
          ||    |  |   |   | | | | | |  || |||   | |||  |   ||         | ||  |       ||| |   || |||  ||||||     ||| || || || |||||||| || ||||||||||| || ||||||| ||| || || |||||| | ||||||||||| ||||||||||||  |  |||   
gtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGAT-GTACGT
















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|31362151|gb|CD446508.1|CD446508
EST:     GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG                         CGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
genomic: GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAGgtgaagttat ... catcctgcagCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
EST: gi|71440938|gb|DR821988.1|DR821988
EST:     GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG                         CGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
genomic: GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAGgtgaagttat ... catcctgcagCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
EST: gi|24763111|gb|CA398294.1|CA398294
EST:     GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG                         CGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
genomic: GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAGgtgaagttat ... catcctgcagCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
EST: gi|76280657|gb|DV020225.1|DV020225
EST:     GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG                         CGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
genomic: GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAGgtgaagttat ... catcctgcagCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
EST: gi|89760515|gb|DY688892.1|DY688892
EST:     GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG                         CGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT
genomic: GCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAGgtgaagttat ... catcctgcagCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttcttgacaccttcagttggttctgaactgtaaaagctctgcatcctgcagCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGTGAAGCAGCACGCGGTGCAGCGAGGGCAGCGTTTTGATGAAAACCGTATA
     tcttgac  putative branch site (score: 3)
                                tgtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagttattactgcctaccgcttcattgatctctcttcttgacaccttcagttggttctgaactgtaaaagctctgcatcctgcagCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGTGAAGCAGCACGCGGTGCAGCGAGGGCAGCGTTTTGATGAAAACCGTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC