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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcctgttgcactgtttgttttcattcttttcatcttcagaactttattaattatgcctttccccattgtccacagGGAGAGAGAAGAGACCGATCAAGTCATTGGTGACAGGCAGGCCAATTCTGCTTGCACTTGAGGATATTGATGGCAGCCCTTCTTTTTTAGAAAAAGCCCT

Basic information

species Zea mays
transcript GRMZM2G115975_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115975_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g24180.1 (Oryza sativa), 3'ss of exon 6
gttagcctg-ttgcactgtttgttttcattcttttcatct-----tcagaactttattaatt--------atgcctttccccattgtccacagGGAGAGAGAAGAGACCGATCAAGTCATTGGTGACAGGCAGGCCAATTCTGCTTGCACTTGAGGATATTGATGGCAGCCCTTCTTTTTTAGAAAAAGCCCT
||| | ||  ||   || |||  |||  || | |||  ||     | | ||| || ||  ||        ||||||||||  ||| |   |||||||||||||||| ||||||||||| || ||    |||||||||||||| || |||||||||||||||||||| |||||||||||| |||||||||| ||
gttggtctacttatgctatttcatttttttttcttctcctactcattacaaccttgtttgttgttaactcatgcctttcca-attatttgcagGGAGAGAGAAGAGGCCGATCAAGTCGTTAGTTGTTGGCAGGCCAATTCTTCTCGCACTTGAGGATATTGATGGAAGCCCTTCTTTTCTAGAAAAAGCTCT
















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|32837002|gb|CD976680.1|CD976680
EST:     CATATGAAGGAGCTATTCCAAATT                         GGAGAGAGAAGAGACCGATCAAGTCATTGGTGACAGGCAGGCCAATTCTGC
genomic: CATATGAAGGAGCTATTCCAAATTgttagcctgt ... ttgtccacagGGAGAGAGAAGAGACCGATCAAGTCATTGGTGACAGGCAGGCCAATTCTGC
EST: gi|50327514|gb|CO522640.1|CO522640
EST:     GATATTTCGTAATGACACAGCTGACACATATGAAGGAGCTATTCCAAATT                         GGAGAGAGAAGAGACCGATCAAGTCATTGGTGACAGGCAGGCCAATTCTGC
genomic: GATATTTCGTAATGACACAGCTGACACATATGAAGGAGCTATTCCAAATTgttagcctgt ... ttgtccacagGGAGAGAGAAGAGACCGATCAAGTCATTGGTGACAGGCAGGCCAATTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcttttcatcttcagaactttattaattatgcctttccccattgtccacagGGAGAGAGAAGAGACCGATCAAGTCATTGGTGACAGGCAGGCCAATTCTGCTTGCACTTGAGGATATTGATGGCAGCCCTTCTTTTTTAGAAAAAGCCCT
                        tattaat  putative branch site (score: 2)
                                   cctttccccattgtcc  putative PPT
                 agaactttattaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcctgttgcactgtttgttttcattcttttcatcttcagaactttattaattatgcctttccccattgtccacagGGAGAGAGAAGAGACCGATCAAGTCATTGGTGACAGGCAGGCCAATTCTGCTTGCACTTGAGGATATTGATGGCAGCCCTTCTTTTTTAGAAAAAGCCCT

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