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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgacaactgaactggaaaactcgtagacggacggttagcacttagcacagtagctacttctgcatttgtcaccacacttttgaagctaaaccaatggtgccaactctcttttgcttttttgtcgaatcgtttattgttgggccactattgtttcag

Basic information

species Zea mays
transcript GRMZM2G087095_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087095_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g54170.1 (Oryza sativa), 5'ss of exon 6
GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgacaactgaactggaaaactcgtagacggacggttagcacttagcacagtagctacttctgcatttgtcaccacacttttgaagctaaaccaatggtgccaactctcttttgcttttttgtcgaatcgtttattgttgggccactattgtttcag
||||||||||| ||||||||||||||||| ||||||||||||||| | ||   |  |  |    || |  ||    ||     | ||  ||| | |  |||| | |||||||||||    |        | |     |   | |  |||                                                      
GAACAAATGCTACAAGATGCAAACAGGGTCCTGAAAAGGAAGgtacgagatttcc-atttactcaaatgctacctagaa----accatatagaaaa--agctccctctgcatttgtagttagggaccgcatgactcgcttcttggacca------------------------------------------------------
















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|211463197|gb|FL126646.1|FL126646
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|32808460|gb|CD960694.1|CD960694
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|74236437|gb|DT644351.1|DT644351
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGC
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGC
EST: gi|78122333|gb|DV540717.1|DV540717
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|50331175|gb|CO526301.1|CO526301
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|32838769|gb|CD978450.1|CD978450
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|18383542|gb|BM416742.1|BM416742
EST:     GACCAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|78112770|gb|DV531164.1|DV531164
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|76285512|gb|DV025080.1|DV025080
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|21809510|gb|BQ667828.1|BQ667828
EST:     TGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: TGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|71425166|gb|DR806565.1|DR806565
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|148951816|gb|EC897579.2|EC897579
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|26557907|gb|CA830142.1|CA830142
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|71421466|gb|DR805441.1|DR805441
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|5055580|gb|AI734467.1|AI734467
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|71330056|gb|DR801767.1|DR801767
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCC
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCC
EST: gi|32847296|gb|CD986977.1|CD986977
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|71421467|gb|DR805442.1|DR805442
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|76285511|gb|DV025079.1|DV025079
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|5030602|gb|AI714796.1|AI714796
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|21809509|gb|BQ667827.1|BQ667827
EST:     GAACAAATGCTGCAAGATGCAAGCAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|32835484|gb|CD975162.1|CD975162
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|71330054|gb|DR801766.1|DR801766
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|87157198|gb|DY401987.1|DY401987
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
EST: gi|71425163|gb|DR806564.1|DR806564
EST:     GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG                         CTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA
genomic: GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAAGGCGAAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgaca ... attgtttcagCTGGGCGAGTTTGAGGCAGAGGCGGCTTCTCCCCCGCAGTTAGCGTGGCAAGGCGAAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAGgtaagtgacaactgaactggaaaactcgtagacggacggttagcacttagcacagtagctacttctgcatttgtcaccacacttttgaagctaaaccaatggtgccaactctcttttgcttttttgtcgaatcgtttattgttgggccactattgtttcag

- - - ATGCTG
- - -  TGCTGC
- - - - -  GCAAGA
- - - - - -  AAGATG
- - - - - - - - - - - - - - - - -  AAGGAA