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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgtagctgcatgatttgtgttctcctgccccattgatgtttcggagccttacatgttctgttttcttggggaaaaatgtgttcctttgcaaggtaacctttctaagtttttttgtgctttgataattgatactcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGTTTTGCACCTACTGAATCGATGATATTGTGTAGATGGACAACCATAATTG

Basic information

species Zea mays
transcript GRMZM2G130548_T03
intron # 5
splice site 3'
intron type U2

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|67010741|gb|CO439490.1|CO439490
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCNGTTTGGANGAAGATGTCTGGATATTANGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|47961743|gb|CN844452.1|CN844452
EST:     TCAATCCAGGATATCAGTACTAGGCAACCATTTTCCCCTTCACTTGCCAG                         NAATGTGCTAG
genomic: TCAATCCAGAATATCAGTACTAGGCAACCATTTTCCC-TTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAG
EST: gi|76292040|gb|DV031608.1|DV031608
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|101383449|gb|EB813780.1|EB813780
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|86472314|gb|DY238684.1|DY238684
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|91877108|gb|EB407065.1|EB407065
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCCCTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|5439382|gb|AI820303.1|AI820303
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|29945353|gb|CB815596.1|CB815596
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|60341409|gb|DN208382.1|DN208382
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|16926976|gb|BM080044.1|BM080044
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|45567900|gb|CK985803.1|CK985803
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|22489673|gb|BU049596.1|BU049596
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTACCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|18649960|gb|BM498779.1|BM498779
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTACCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|87153170|gb|DY397959.1|DY397959
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTACCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|211470172|gb|FL446046.1|FL446046
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|211320303|gb|FL454022.1|FL454022
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|50337772|gb|CO532898.1|CO532898
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|32865321|gb|CF005003.1|CF005003
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|211023896|gb|FL457615.1|FL457615
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|19822487|gb|BQ048511.1|BQ048511
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTACCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaggtaacctttctaagtttttttgtgctttgataattgatactcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGTTTTGCACCTACTGAATCGATGATATTGTGTAGATGGACAACCATAATTG
            tttctaagttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgtagctgcatgatttgtgttctcctgccccattgatgtttcggagccttacatgttctgttttcttggggaaaaatgtgttcctttgcaaggtaacctttctaagtttttttgtgctttgataattgatactcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGTTTTGCACCTACTGAATCGATGATATTGTGTAGATGGACAACCATAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA