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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtccatcttcttagtttgcccatgttacaacagtgcatcattcatttaatcattttcattacaacttggtaaactggaagtttaatgtgctctttttcctttatctgtctctgcaataacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG

Basic information

species Zea mays
transcript GRMZM5G868168_T03
intron # 4
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|50324151|gb|CO519277.1|CO519277
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|78120174|gb|DV538558.1|DV538558
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|154130463|gb|EC872173.2|EC872173
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|148986921|gb|EE030732.2|EE030732
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|78103984|gb|DV522402.1|DV522402
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|76931706|gb|DV172823.1|DV172823
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|149004790|gb|EE039293.2|EE039293
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|91048130|gb|EB158548.1|EB158548
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|31356046|gb|CD440403.1|CD440403
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|31350150|gb|CD434507.1|CD434507
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|149078033|gb|EE166771.2|EE166771
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|149080766|gb|EE169831.2|EE169831
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|33467141|gb|CF244190.1|CF244190
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|19057652|gb|BM736319.1|BM736319
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
EST: gi|211065956|gb|FK946601.1|FK946601
EST:     GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG                         GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG
genomic: GAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAGgttgtccatc ... taacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactggaagtttaatgtgctctttttcctttatctgtctctgcaataacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG
                                          caataac  putative branch site (score: 2)
      aagtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtccatcttcttagtttgcccatgttacaacagtgcatcattcatttaatcattttcattacaacttggtaaactggaagtttaatgtgctctttttcctttatctgtctctgcaataacaagcagGGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT