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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgcaagattttgattgaccacataactcatttgtgtgttactttgatacttcagtacatggtaccgatctcaaacatgttgtttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAG

Basic information

species Zea mays
transcript GRMZM5G860137_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G860137_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g02020.1 (Oryza sativa), 3'ss of exon 5
gtgcgtgcaagattttgattgacc--acataactcatttgtgtgttactttgatacttcagtacatggtaccgatctca---aacatgttg--tttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAG
||| ||  |  |||| ||  ||||  | ||   |  | |   ||  |  |  | ||||||||   ||| || ||| |||   |||||  ||  |||  ||||||||||||||||| |||||||||||||||||| || |||||||||||||||||||||||||||||
gtgggtatataatttggaccgacctaaaattggttttctacatgacatatcaacacttcagtcactggcacagatttcataaaacattctggatttttcagGTTGAAATTTCTTCCGGTAGAGGGAAACCACCACTTATTGTTGACAAGGATGAGAGTCTTGCAAAG
















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|78180536|gb|DV551029.1|DV551029
EST:     GTGGCATAGCAGCTCGGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT                         GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGAT
genomic: GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCTgtgcgtgcaa ... tgtttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGAT
EST: gi|71426143|gb|DR807193.1|DR807193
EST:     GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT                         GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGGTGTTGACAAGGAT
genomic: GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCTgtgcgtgcaa ... tgtttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGAT
EST: gi|71439486|gb|DR820536.1|DR820536
EST:     GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT                         GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTT
genomic: GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCTgtgcgtgcaa ... tgtttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTT
EST: gi|6994169|gb|AW453383.1|AW453383
EST:     GTGGCATAGCAGCTCGGGATAGCGGTGCATTTTCTTGGGAGATTGTTCCT                         GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGAT
genomic: GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCTgtgcgtgcaa ... tgtttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGAT
EST: gi|12047245|gb|BF729384.1|BF729384
EST:     GTGGCATAGCAGCTCGGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT                         GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGAT
genomic: GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCTgtgcgtgcaa ... tgtttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGAT
EST: gi|89760643|gb|DY688974.1|DY688974
EST:     GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCT                         GTTTGAA-TTTCTTCTG
genomic: GTGGCATAGCAGCTCAGGACAGCGGTGCATTTTCTTGGGAGATTGTTCCTgtgcgtgcaa ... tgtttcccagGTT-GAAATTTCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttactttgatacttcagtacatggtaccgatctcaaacatgttgtttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAG
      ctttgat  putative branch site (score: 5)
                                            ttgtttccc  putative PPT
       tttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgcaagattttgattgaccacataactcatttgtgtgttactttgatacttcagtacatggtaccgatctcaaacatgttgtttcccagGTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG