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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttacatcctctttaaattttggctctggtatttttcttattttcagtggtttttaatacttctagtgttgcctaaagtatttttgacatcatatccataatattctgcatgttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG

Basic information

species Zea mays
transcript GRMZM2G171745_T02
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|13178371|gb|BG349629.1|BG349629
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|60346665|gb|DN213638.1|DN213638
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|211178527|gb|FK980685.1|FK980685
EST:     AAATGTAAGAGAACTCGAAGATT-CCTAAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAA
genomic: AAATGTAAGAGAACTCGAAGATTTCCTAA-TCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAA
EST: gi|78118434|gb|DV536820.1|DV536820
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|211178524|gb|FK980682.1|FK980682
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|211195518|gb|FL100642.1|FL100642
EST:     TAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: TAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|86472725|gb|DY239095.1|DY239095
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAAGTGAATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|211180926|gb|FK980688.1|FK980688
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|71427328|gb|DR808378.1|DR808378
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|148943925|gb|EC889005.2|EC889005
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|148972927|gb|EE023942.2|EE023942
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|78081417|gb|DV509829.1|DV509829
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCC                         GGTATCGTTAGAGGCAAACTGGA
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGA
EST: gi|78112152|gb|DV530548.1|DV530548
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|74242379|gb|DT650293.1|DT650293
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|149089443|gb|EE178684.2|EE178684
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|211178525|gb|FK980683.1|FK980683
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|76931006|gb|DV172592.1|DV172592
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|78118433|gb|DV536819.1|DV536819
EST:     CAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|5268890|gb|AI770854.1|AI770854
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAG
EST: gi|211180929|gb|FK980691.1|FK980691
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|29129753|gb|CB380457.1|CB380457
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|71427327|gb|DR808377.1|DR808377
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|78112153|gb|DV530549.1|DV530549
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAA-GGTGCTTTGAG
EST: gi|31352916|gb|CD437273.1|CD437273
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
EST: gi|50339563|gb|CO534689.1|CO534689
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGGTACAA
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGGTACAA
EST: gi|67021495|gb|CO450244.1|CO450244
EST:     CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG                         GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
genomic: CAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCGgtgagttgtt ... gttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcctaaagtatttttgacatcatatccataatattctgcatgttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
               ttttgac  putative branch site (score: 3)
       taaagtatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttacatcctctttaaattttggctctggtatttttcttattttcagtggtttttaatacttctagtgttgcctaaagtatttttgacatcatatccataatattctgcatgttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA