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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttccttaactctattacctctcccagcggttgccatttttttttgtcataccctttttttgctcccctttctgtttgtaataataacttgtgctcaaaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTTGGAAAGCATGCATTCTAAAGG

Basic information

species Zea mays
transcript GRMZM2G017835_T01
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|31355100|gb|CD439457.1|CD439457
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|211242969|gb|FL282602.1|FL282602
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATNTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|22819487|gb|BU499577.1|BU499577
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|211242967|gb|FL282600.1|FL282600
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|76015692|gb|DT942862.1|DT942862
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|76285882|gb|DV025450.1|DV025450
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCA
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCA
EST: gi|32832258|gb|CD971936.1|CD971936
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|87156608|gb|DY401397.1|DY401397
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|31440950|gb|CD510381.1|CD510381
EST:     GATATGCTGGGG-CTAGTTTG-GGGATTCATGGAATTCATT-GGCCAATC                         CATGCCATCGGAAATGG-GGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|6587599|gb|AW244917.1|AW244917
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|6865178|gb|AW360528.1|AW360528
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|32832272|gb|CD971950.1|CD971950
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|211242968|gb|FL282601.1|FL282601
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|148939514|gb|EC884102.2|EC884102
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|26559748|gb|CA831983.1|CA831983
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|32832300|gb|CD971978.1|CD971978
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|148988749|gb|EE031658.2|EE031658
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|60345255|gb|DN212228.1|DN212228
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|32832043|gb|CD971721.1|CD971721
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|32835538|gb|CD975216.1|CD975216
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
EST: gi|32835900|gb|CD975578.1|CD975578
EST:     GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATC                         CATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT
genomic: GATATGCTGGGGCCTAGTTTGTGGGATTCATGGAATTCATTAGGCCAATCgtgagttcct ... aaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttttttgctcccctttctgtttgtaataataacttgtgctcaaaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTTGGAAAGCATGCATTCTAAAGG
                             taataac  putative branch site (score: 1)
                                                cttcc  putative PPT
                      tttgtaataataactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttccttaactctattacctctcccagcggttgccatttttttttgtcataccctttttttgctcccctttctgtttgtaataataacttgtgctcaaaacttccagCATGCCATCGGAAATGGTGGCTTGCATTGCCATGGAGTCCATTTCCATCTTGGAAAGCATGCATTCTAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA