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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttattttttcaaaattttaacatgtgtaattctgttctatcactcaataaaataaccaatattctttgtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCAACTCGAAAAATAAG

Basic information

species Zea mays
transcript GRMZM2G068755_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 5
---------------gtgcgttattttttcaaaattttaacatgtgtaattctgttctatcactcaataaaataaccaatattctttgtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCAACTCGAAAAATAAG
                   |  |||    ||  ||    ||||   | ||  ||| |  |  || ||||  |||| ||   || ||  |||||  ||||||| || |||||||||||| | |||||||| || ||| | |||||||||||||| || |||||
gtacaatatttcataccaggccattagagcagcatgcacacattgatcata-tgtaccttgcctgaatagtataatcacacttattcctgtttgtagAAAAAAGAATTGGAAGCAGAGCTAGCAAATGTCTCAGGAATCGCTAAGCCAACTCGCAAGATAAG
















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|211517040|gb|FL438272.1|FL438272
EST:     GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATG                         AAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
genomic: GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
EST: gi|71441120|gb|DR822170.1|DR822170
EST:     GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATG                         AAAAAGGAGTTG
genomic: GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTG
EST: gi|18963448|gb|BM660440.1|BM660440
EST:     GCAAAGCCCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATG                         AAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
genomic: GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
EST: gi|32934909|gb|CF039721.1|CF039721
EST:     GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATG                         AAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
genomic: GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA

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), 48 (downstream exon)
Score: 88

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCAACTCGAAAAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCAACTCGAAAAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 23

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCAACTCGAAAAATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCAACTCGAAAAATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtaattctgttctatcactcaataaaataaccaatattctttgtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCAACTCGAAAAATAAG
                           aaataac  putative branch site (score: 78)
                                       ttctttgt  putative PPT
                       aataaaataaccaata  TA-rich tract