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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattaaaaggctattcctgttttctcctgaaattcggaatgccgcaccatgtttctatccaagtaactcctttatgcatgtcttcatttgggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG

Basic information

species Zea mays
transcript GRMZM2G087095_T01
intron # 4
splice site 3'
intron type U2

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:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|50331176|gb|CO526302.1|CO526302
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|74236437|gb|DT644351.1|DT644351
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|78122333|gb|DV540717.1|DV540717
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|50331175|gb|CO526301.1|CO526301
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|32838769|gb|CD978450.1|CD978450
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|78112770|gb|DV531164.1|DV531164
EST:     TCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: TCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|76285512|gb|DV025080.1|DV025080
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|71425166|gb|DR806565.1|DR806565
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|71421466|gb|DR805441.1|DR805441
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|5055580|gb|AI734467.1|AI734467
EST:     AGCTTGAGAATCAAGTAGCCAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|71330056|gb|DR801767.1|DR801767
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|32847296|gb|CD986977.1|CD986977
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|71421467|gb|DR805442.1|DR805442
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|76285511|gb|DV025079.1|DV025079
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|32835484|gb|CD975162.1|CD975162
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|71330054|gb|DR801766.1|DR801766
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
EST: gi|71425163|gb|DR806564.1|DR806564
EST:     AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
genomic: AGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG

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: 42 (upstream exon), 48 (downstream exon)
Score: 108

GAATCTTCTTGGTGAAGATCTGGCCCTACTTAGCCCAAGTGAACTTGACCAGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG


Block sizes: 42 (upstream exon), 25 (downstream exon)
Score: 33

GAATCTTCTTGGTGAAGATCTGGCCCTACTTAGCCCAAGTGAACTTGACCAGCTTGAGAATCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaagtaag ... ggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatgtttctatccaagtaactcctttatgcatgtcttcatttgggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG
               aagtaac  putative branch site (score: 33)
      tttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattaaaaggctattcctgttttctcctgaaattcggaatgccgcaccatgtttctatccaagtaactcctttatgcatgtcttcatttgggtttggcagACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - attcctg
- - - - - - - - - - - tctcctg
- - - - - - - - - - - - - - - - - - - - gccgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcattt