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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatgagggagagatagttcttcaattgtactcttcagacttcttttataccatattcttcaccaatatcacattagctttgttgctttcttggcagcttacttataattgtttctattcacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA

Basic information

species Zea mays
transcript GRMZM2G158097_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158097_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g36062.1 (Oryza sativa), 3'ss of exon 8
gtaattat--gagggagagatagttcttcaattgtactcttcagacttcttttataccat-----attctt-------cacca--atatcacattagctttgttgctttctt--------------ggca------------gcttacttataattgtttctattcacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA
||  | ||   | | |   ||  ||||     || ||| |      ||  ||||   |||     || |||       || ||  |||||   || | |||| |  |||  |              ||||              | |||||| ||  ||| | ||  | |||||||||   || ||||||||||| ||||| |||||||| |||||||||||||||||
gtgctcattttatgaatgaatgattctgtggctgcactatattcgttttctttacttcatcgaatatgctttagttaacatcagcatatcctctttgatttgctatttttctttacattttgagaaggcacttacatattccattcacttatcatgatttttctttgctttgcagAGCGAGCATTGGGACACCTTTTATAAGTTCTACCGCAACACAACTGATAATCA
















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|32841147|gb|CD980828.1|CD980828
EST:     TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAG                         AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
genomic: TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
EST: gi|32840869|gb|CD980550.1|CD980550
EST:     TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAG                         AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
genomic: TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
EST: gi|13389377|gb|BG462692.1|BG462692
EST:     TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAG                         AGCAGATTTTTTGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
genomic: TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
EST: gi|32841581|gb|CD981262.1|CD981262
EST:     TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAG                         AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
genomic: TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
EST: gi|32841639|gb|CD981320.1|CD981320
EST:     TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAG                         AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT
genomic: TTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAAT

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: 45 (upstream exon), 48 (downstream exon)
Score: 37

ATTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 41

ATTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA


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

ATTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

ATTCCTGCCCAAAATTTGCAAATGAAGCGACTTCGTGGAGACGAAATAAAGgtaattatga ... cacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctttgttgctttcttggcagcttacttataattgtttctattcacattgcagAGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA
                     agcttac  putative branch site (score: 45)
                                     tttctattc  putative PPT
                        ttacttataattgttt  TA-rich tract