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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtctgtttctgacgcaacaatcacgtcagcatgacacacagcatatatcattactgtgttctaagtgcacgcccataacgcatatgcacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACGGCCCGGCGGCGGGGCGTGGACCTGGTGGTGGTGAACCCCGTGCTGGTGG

Basic information

species Zea mays
transcript GRMZM2G131205_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131205_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g34280.1 (Oryza sativa), 3'ss of exon 3
ttttgtctgtttctgacgcaacaatcacgtcagcatgacacacagcatatatcattactgtgttctaagtgcacgcccataacgcatatgca----cgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACGGCCCGGCGGCGGGGCGTGGACCTGGTGGTGGTGAACCCCGTGCTGGTGG
         |||  |   ||||| | |  |  | |  |      |||    | | | ||||    |||  | |     | ||   ||||| |     | |||||||||||||||||||||| |||||||||||||||||||||||||||||| |||| |||||||| || ||||| ||||||||||||||||| ||||||||| 
---caggactttgcgcttcaaca-taagctacgaacaattatttgcaatacttaatcctgtaaagtaaaagaaaatgaaaaaaatatatgaaatgatggtgcagAACTGGTACTGCTACGGGAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGGCGGCGCGGCGGCGAGGGGTGGAGCTGGTGGTGGTGAACCCGGTGCTGGTGA

upper sequence: GRMZM2G131205_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0070g00240.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------------------------------------ttttgtctgtttctgacgcaacaatcacgtcagcatgacacacagcatatatcattactgtgttctaagtgcacgcccataacgcat---atgcacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACGGCCCGGCGGCGGGGCGTGGACCTGGTGGTGGTGAACCCCGTGCTGGTGG
                                                                                              |      ||| | | | |   |||      | | | | |||  |  ||| |   | |||     | ||    |      | |   |      | |   ||||||| ||||| || ||||| ||||||||||||||||||||||| ||||||   ||   |  |   |  |||||||| |||||||||||||| ||||||||| 
gtcttcccacctatctttttttcttcaacactatttacccctaattttcatcattttttttcaacattttcgcttcttcttcaacctataatcatcagacttgtctttcatgtcccaaaggtaacggaacggcac-taaaataaaatttgact-cacccaaaaacaagatttttgattaactgagaggaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTTGCGAAGGAGAAAGAGGTGGACCTTGTGGTGGTGAACCCAGTGCTGGTGC

upper sequence: GRMZM2G131205_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0070g00240.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------------------------------------ttttgtctgtttctgacgcaacaatcacgtcagcatgacacacagcatatatcattactgtgttctaagtgcacgcccataacgcat---atgcacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACGGCCCGGCGGCGGGGCGTGGACCTGGTGGTGGTGAACCCCGTGCTGGTGG
                                                                                              |      ||| | | | |   |||      | | | | |||  |  ||| |   | |||     | ||    |      | |   |      | |   ||||||| ||||| || ||||| ||||||||||||||||||||||| ||||||   ||   |  |   |  |||||||| |||||||||||||| ||||||||| 
gtcttcccacctatctttttttcttcaacactatttacccctaattttcatcattttttttcaacattttcgcttcttcttcaacctataatcatcagacttgtctttcatgtcccaaaggtaacggaacggcac-taaaataaaatttgact-cacccaaaaacaagatttttgattaactgagaggaaaatgcagAATTGGTATTGTTACGGAAAGGCGGTGGCGGAGCAGGCGGCATGGGAGGTTGCGAAGGAGAAAGAGGTGGACCTTGTGGTGGTGAACCCAGTGCTGGTGC

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|71757837|gb|DR955774.1|DR955774
EST:     TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGG                         AACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
genomic: TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGGgtgggtgtgc ... cacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
EST: gi|211185933|gb|FL216419.1|FL216419
EST:     TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGG                         AACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
genomic: TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGGgtgggtgtgc ... cacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
EST: gi|211183533|gb|FL216412.1|FL216412
EST:     TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGG                         AACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
genomic: TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGGgtgggtgtgc ... cacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
EST: gi|211280839|gb|FL066043.1|FL066043
EST:     TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGG                         AACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
genomic: TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGGgtgggtgtgc ... cacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
EST: gi|78122451|gb|DV540835.1|DV540835
EST:     TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGATCTGCGAGAAAACCAGG                         AACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
genomic: TGGTCGACGAGTCGTGCTGGAGCGACCTCGAGTTCTGCGAGAAAACCAGGgtgggtgtgc ... cacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
EST: gi|78079587|gb|DV507999.1|DV507999
EST:     GAGAAAACCAGG                         AACTGGTACTGCTACGCCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
genomic: GAGAAAACCAGGgtgggtgtgc ... cacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACG
EST: gi|71328290|gb|DR800775.1|DR800775
EST:     AGAAAACCAGG                         AACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCA-GCGGGCGTGGGAGAC
genomic: AGAAAACCAGGgtgggtgtgc ... cacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGC-GGCGTGGGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatatcattactgtgttctaagtgcacgcccataacgcatatgcacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACGGCCCGGCGGCGGGGCGTGGACCTGGTGGTGGTGAACCCCGTGCTGGTGG
                               ccataac  putative branch site (score: 3)
     atcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtctgtttctgacgcaacaatcacgtcagcatgacacacagcatatatcattactgtgttctaagtgcacgcccataacgcatatgcacgctgcagAACTGGTACTGCTACGGCAAGGCGGTGGCGGAGCAGGCGGCGTGGGAGACGGCCCGGCGGCGGGGCGTGGACCTGGTGGTGGTGAACCCCGTGCTGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG