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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctagattatgatttctatctgtgtcgtttgctacattggattcagtggcttgacaacaaaattgttacattactgtcatacttcttgatgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGA

Basic information

species Zea mays
transcript GRMZM2G170291_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170291_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g18200.1 (Oryza sativa), 3'ss of exon 2
--------tcctagattatgatttctatctgtgtcgtttgctacattggattcagtggcttgacaacaaaattgttacattactgtcatacttcttgatgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGA
          ||   || || |  ||   ||    ||||  || |||| |||   ||   |  | |  ||||||||    ||   ||| |  ||| |||| || ||||||||| || |||||||||||   | ||||||| |||||||| ||||||||||||||||||||||| || |||||||| || ||||||||| |||||||||
aagctacagtcttttttttggtcccttcatg-actgtttagtatattgcatttgttgtgct--ccaagaaattgtt---ctaagatcaca--tctcgatgccatgcagGTAGTGCTGCGTGCTTTGTCGAGTCCACCTTTTAAAGACTATCGTGTCTGGTGGTCTCTTTCAGACTCCAAATATGCAGGCACAGCTATGATTATAAAGA

upper sequence: GRMZM2G170291_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G36610.1 (Glycine max), 3'ss of exon 2
tcctagattatgatttctatctgtgtcgtttgctacattggattcagtggcttgacaacaaaattgttacattactgtcatacttcttgatgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGA
|  |  |  |  |  |  |           || ||  ||  ||| |     |   ||    | ||  ||   |  || || | || || |  | | |||| |  |   ||||||  | || ||| |||||||     |||| |  || |||||||||||| |||||||||| ||||| ||||||||  |  |  | || |
ttatgcaccaaaacatgaacaaaacgatactgttatgttcaattgatataatcatcatattactttctattATTTTGACACATTTGTTTAACTTATGCAGATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGGTGGTCTCTTGCAGATTCAAAGTATGCAGGGACAGCACTACTGGTGAAAA

upper sequence: GRMZM2G170291_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g09970.t01 (Vitis vinifera), 3'ss of exon 2
tcctagat-tatgatttctatctgtgtcgtttgctacattgg-attcagtggcttgacaacaaaattgttacattactgtcatacttcttgatgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGA
|    | | | ||| ||   |    |   |||| ||  |      | ||    | |   |   | |     || |  | | ||   | ||||   || |||| || |  | | |||  | ||     | || ||   | | || ||||| |||||||||||| ||||||| |||||||| ||||| ||  ||||| | ||||
tttgggctctgtgagttgagttgtggaaatttggtatttcaacgctaagaaaatcggatatctactaacagcaattatat-atttcttttga-accatgcagATATTAATGCATGCCCTTTCCAGACCTCCATTTGGAAATTATCGTGTTTGGTGGTCTCTTGCAGATTCCAAATATGCAGGGACTGCATTGTTTGTTAAGA

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|211261839|gb|FL294946.1|FL294946
EST:     ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG                         GTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAA
genomic: ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAGgttttttggc ... tgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAA
EST: gi|211321949|gb|FK966255.1|FK966255
EST:     ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG                         GTAGTTCTACGTGCTTTGTCAGCTTCASCTTTCAAAGACTACCGTGTCTGG
genomic: ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAGgttttttggc ... tgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
EST: gi|211194081|gb|FL030608.1|FL030608
EST:     ACCCCAGTGAACTAAAAGATGACACAAGCTCGTCACGGGATGAAAAGCAG                         GTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
genomic: ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAGgttttttggc ... tgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
EST: gi|211471748|gb|FL295692.1|FL295692
EST:     ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG                         GTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
genomic: ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAGgttttttggc ... tgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
EST: gi|211194080|gb|FL030607.1|FL030607
EST:     ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG                         GTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
genomic: ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAGgttttttggc ... tgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
EST: gi|91873537|gb|EB403494.1|EB403494
EST:     ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG                         GTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
genomic: ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAGgttttttggc ... tgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
EST: gi|211194082|gb|FL030609.1|FL030609
EST:     ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG                         GTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
genomic: ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAGgttttttggc ... tgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
EST: gi|89757612|gb|DY687140.1|DY687140
EST:     ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG                         GTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG
genomic: ACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAGgttttttggc ... tgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtggcttgacaacaaaattgttacattactgtcatacttcttgatgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGA
                                       tcttgat  putative branch site (score: 4)
              aaaattgttacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctagattatgatttctatctgtgtcgtttgctacattggattcagtggcttgacaacaaaattgttacattactgtcatacttcttgatgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG