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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttgctttgtttaatctaatttccttgggtattgatacagcaaaagctcacatttgtttgtttattttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG

Basic information

species Zea mays
transcript GRMZM2G120857_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 7
gtaaacttgct-ttgtttaatctaatttccttgggtattgatacagcaaaagctcacatttgtttgtttattttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG
||||| ||| | ||||||  ||||      |    |   | ||   |||   |    |  | ||| |  | | |||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
gtaaatttgttattgtttgttctatcaatttgacatccaggtaatacaacgccaactaactattt-tgcactctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG
















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|37380928|gb|CF627310.1|CF627310
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|76019790|gb|DT946960.1|DT946960
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|211101475|gb|FL457329.1|FL457329
EST:     ATTAGTGATCTATGTGCTGG-TTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|110194437|gb|EC876335.1|EC876335
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|211216460|gb|FL469131.1|FL469131
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTT-TCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|31250098|gb|CD219122.1|CD219122
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGTAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|74239665|gb|DT647579.1|DT647579
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|23199568|gb|BU582133.1|BU582133
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|87155757|gb|DY400546.1|DY400546
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|29544695|gb|CB605075.1|CB605075
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|32915735|gb|CF020547.1|CF020547
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|33103704|gb|CF063664.1|CF063664
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|16925630|gb|BM078698.1|BM078698
EST:     CGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: CGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|211039065|gb|FL478477.1|FL478477
EST:     AGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: AGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|29167895|gb|CB411155.1|CB411155
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|9731686|gb|BE510438.1|BE510438
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTG
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTG
EST: gi|211333619|gb|FL125157.1|FL125157
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGG
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGG
EST: gi|166704216|gb|EG154128.1|EG154128
EST:     CCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: CCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|37381420|gb|CF627593.1|CF627593
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|37384800|gb|CF629499.1|CF629499
EST:     NTTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: -TTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|31250137|gb|CD219161.1|CD219161
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGTAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
EST: gi|78109385|gb|DV527801.1|DV527801
EST:     ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAG                         TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC
genomic: ATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTC

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), 49 (downstream exon)
Score: 159

ATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

ATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

ATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

ATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaaacttgc ... attttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttccttgggtattgatacagcaaaagctcacatttgtttgtttattttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG
                          agctcac  putative branch site (score: 330)
                                      tttgtttattttccc  putative PPT
                                 atttgtttgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacttgctttgtttaatctaatttccttgggtattgatacagcaaaagctcacatttgtttgtttattttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT