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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggtagtacatgtcatccacgcttgaagcgttctacccttcaagtaagtccttgtactatttgccgcccctctcaactttttagtgtttattttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG

Basic information

species Zea mays
transcript GRMZM2G066051_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 8
-gaggtagtacatgtcatccacgcttgaagcgttctacccttcaagtaagtccttgtactatttgccgcccctctcaactttttagtgtttattttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
  | |      |  | || ||   |  | || ||  |  ||   || |  |   | |   |           | |||    || |    ||   ||  |||||||| || |||||||||||||||||||||||||| |||||||||
taatggccccaagattattcaaa-tcaaggcatttcagactatcagcatttttctttctgagaaattcatattatcatggattcatctcttgaattttcagGATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAG
















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|37401622|gb|CF638179.1|CF638179
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|166669627|gb|EG155792.1|EG155792
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACG
EST: gi|5597279|gb|AI891272.1|AI891272
EST:     GCTATGTTAGCTCCAAAGACANCCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|148999213|gb|EE036132.2|EE036132
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|149082295|gb|EE171480.2|EE171480
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|111192096|gb|EE290232.1|EE290232
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|37386784|gb|CF630581.1|CF630581
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|5714302|gb|AI944287.1|AI944287
EST:     GCTATGTTAGCTCCAAAG-CAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|149041351|gb|EE046989.2|EE046989
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|78107218|gb|DV525636.1|DV525636
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|86475161|gb|DY241531.1|DY241531
EST:     GCTATGTTAGCTCCAAAGCCAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTGGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|148931817|gb|EC877263.2|EC877263
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|33467028|gb|CF244077.1|CF244077
EST:     GCTATGTTAGCTCCAAAGACACCCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|60354560|gb|DN221533.1|DN221533
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|16377803|gb|BI992125.1|BI992125
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|5895944|gb|AW037190.1|AW037190
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|14202201|gb|BG835878.1|BG835878
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|6056704|gb|AW091109.1|AW091109
EST:     GCTATGTTAGCTCCAAAGNCAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|6445388|gb|AW179351.1|AW179351
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|6056599|gb|AW091004.1|AW091004
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|3157331|gb|AA979953.1|AA979953
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|5525422|gb|AI861315.1|AI861315
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|110518192|gb|EE022779.1|EE022779
EST:     GCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTGGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|24769447|gb|CA404576.1|CA404576
EST:     GCTATGTTAGCTCCAAAGACACCCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|60350125|gb|DN217098.1|DN217098
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|211020659|gb|FL429513.1|FL429513
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTGTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
EST: gi|71328879|gb|DR801122.1|DR801122
EST:     GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGG                         GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
genomic: GCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 99

TTGTTGGGAGATATGCTGCTGGATAGATCAAATGCTGCAGTCATGATGCGCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 184

TTGTTGGGAGATATGCTGCTGGATAGATCAAATGCTGCAGTCATGATGCGCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 148

TTGTTGGGAGATATGCTGCTGGATAGATCAAATGCTGCAGTCATGATGCGCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 183

TTGTTGGGAGATATGCTGCTGGATAGATCAAATGCTGCAGTCATGATGCGCTATGTTAGCTCCAAAGACAACCTTATGATTTTGATGAATCTCTTAAGGgtcagtgtac ... attttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtccttgtactatttgccgcccctctcaactttttagtgtttattttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG
                                          tttatttt  CT-rich tract
                                 tttttagtgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggtagtacatgtcatccacgcttgaagcgttctacccttcaagtaagtccttgtactatttgccgcccctctcaactttttagtgtttattttgccagGATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - gtacatg
- - - - - - - catccac
- - - - - - - - - - - - - - - - - - cccttca
- - - - - - - - - - - - - - - - - - - - - - - - gtccttg