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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatgctgcctattttcattcgatcctgctaattactttgtttcattctcattgatctatttgctttggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTACACCTTTGAACAAGTCGACCATGACAAGTGATGAGTATAAGAATGCTGTT

Basic information

species Zea mays
transcript GRMZM2G161337_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g15780.1 (Oryza sativa), 3'ss of exon 4
gtaagctatgctgcctattttcattcgatcctg-------ctaatt--actttg----tttcattctcattgatctatttgctttggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTACACCTTTGAACAAGTCGACCATGACAAGTGATGAGTATAAGAATGCTGTT
||||||||  |||      ||| ||| ||||||       ||||||   |||||    |  ||   ||  |    |||||  |||  | | ||| ||||  || ||||| |||||||| ||| | ||||| ||  |||||||||||||||||||||| || |||||||||||||||||||| ||||||||||||
gtaagctaacctgtgcccattccttcaatcctgtgttttgctaattctgctttggtgctcacagcttctatatcttatttcattttcactccagACCCAAGCTTTCTCCAGGATTTGTAAAGTTACACACTCGGCAGTTTGGTACACCTTTGAACAAATCAACCATGACAAGTGATGAGTACAAGAATGCTGTT
















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|6021162|gb|AW066090.1|AW066090
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|380469195|gb|JK784390.1|JK784390
EST:     GGCAGGTCCCGACTGAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACGCTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGATTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|60401378|gb|DN234185.1|DN234185
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|32846234|gb|CD985915.1|CD985915
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCTTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|31364516|gb|CD448871.1|CD448871
EST:     GCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|5901211|gb|AW042311.1|AW042311
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|60400588|gb|DN233395.1|DN233395
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|32798334|gb|CD950570.1|CD950570
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|71447101|gb|DR828151.1|DR828151
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|5915491|gb|AW053132.1|AW053132
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|211280784|gb|FL175927.1|FL175927
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
EST: gi|32795466|gb|CD947702.1|CD947702
EST:     GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGT                         CCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC
genomic: GGCAGGTCCCGACTAAACATGTTGCTATCTAAAGTGCACAATTCCAATGTgtaagctatg ... tggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcctgctaattactttgtttcattctcattgatctatttgctttggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTACACCTTTGAACAAGTCGACCATGACAAGTGATGAGTATAAGAATGCTGTT
                                      tttgcttt  CT-rich tract
        taattactttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctatgctgcctattttcattcgatcctgctaattactttgtttcattctcattgatctatttgctttggatttcagCCCCACACTCTCTCCTGGATTTGTGAAGCTGCACACACGCAAGTTTGGTACACCTTTGAACAAGTCGACCATGACAAGTGATGAGTATAAGAATGCTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT