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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtatgtttcgaaccacctcggtttttataaaccagtttcttaaaaactgggtgcttccaaataggcctttaatgaagttcttttctaataaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG

Basic information

species Zea mays
transcript GRMZM2G442404_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G442404_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g15594.1 (Oryza sativa), 3'ss of exon 6
tagtatgtttcgaaccacctcggtttttataaaccagtttcttaaaaa--ctgggtgcttccaaataggcctttaatgaagttc------ttttctaataaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG
        ||| |     |||  ||| ||| |  |   | ||  | ||  |||       ||| ||||    |   ||||| |       | |  ||| ||| | ||||||||||   ||| ||| ||  |||||||||| ||||| ||||| || || ||||||||||| ||||||||||||
------agttcaacttgtctc--tttgtatgactcctctgctgtataattctgatcatgaccatatagcttgtgtgtgaagcttgattaatgtcttaagaaattacagGAAGAACTTGTCAATGAAGACTTGGAATGCCTCGTTCTTGCTAGCGATGGACTTTGGGATGTCGTGGAAAATGAG
















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|37398527|gb|CF636579.1|CF636579
EST:     TGTGTTGGGGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|4776156|gb|AI665159.1|AI665159
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|211024205|gb|FL472254.1|FL472254
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|32863266|gb|CF002948.1|CF002948
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|32925505|gb|CF030317.1|CF030317
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|148973759|gb|EE024892.2|EE024892
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACGTGAAATTCAG                         GAAGAACAGTTCAGGGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|149107129|gb|EE189018.2|EE189018
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|71307033|gb|DR789670.1|DR789670
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|149107130|gb|EE189019.2|EE189019
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
EST: gi|149051712|gb|EE155827.2|EE155827
EST:     TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAG                         GAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG
genomic: TTGGCAATCGTTTACTGAAGCCATATGTGGTGGCGGAACCTGAAATTCAGgtgagaatct ... taaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactgggtgcttccaaataggcctttaatgaagttcttttctaataaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG
                                       ttctaat  putative branch site (score: 2)
                                  ttcttttctaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtatgtttcgaaccacctcggtttttataaaccagtttcttaaaaactgggtgcttccaaataggcctttaatgaagttcttttctaataaactgcagGAAGAACAGTTCAGTGATGAGCTGGAATGCCTGGTTCTCGCTAGTGACGGGCTTTGGGATGTTGTGGAAAATGAG

- - atgtttc
- - - - - - aaccacc
- - - - - - - - - - - - - - - - - - - - - -aaaaactg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttcc