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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaatctacctgtctaataagtaagagcaaattaatgcatttttagtgggtgcaccattaaccttaataatattctaaagtagaaacctcctgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG

Basic information

species Zea mays
transcript GRMZM2G053531_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053531_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 6
gtacaaatctacc-tgtctaataagtaagagcaaattaatgcatttttagtgggtgcaccattaaccttaataatattctaaagtagaaacctcctgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG
||||  ||  |     | |  |||  | ||  || | ||  ||  ||||||| || ||  | || | ||||    ||| |||| |||||||  |||  |||||||||   ||| | |||||| |  |||||||| |||||  | ||||||||||||||||||||||||||||| ||||||
gtacttatgcagagcattttttaaaaagga--aactgaactcaactttagtgtgtacaatactatcattaac--cattttaaactagaaactgcctatactgcagGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG

upper sequence: GRMZM2G053531_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g12960.t01 (Vitis vinifera), 3'ss of exon 7
--------gtacaaatctacctgtctaataagtaagagcaaattaatgcatttttagtgggtgca--ccattaaccttaataatattctaaagtagaaacctcctgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG
         | |    |  | |||    ||| | |  ||    |  | | |  |||| || | ||    || ||     || || ||   | || ||            |||||||   | ||   | ||| | | |||  || || ||||| |||||||||||||| |||||||||||| | ||||||
gcatattcctgctgtaccccttgttctttaattgattgc---cttgtacttcattagaggatacaggtgatcaattgacatgatgttg-gatgtgga------------tgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG
















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|60353122|gb|DN220095.1|DN220095
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|84969850|gb|DW468264.1|DW468264
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|60358119|gb|DN225092.1|DN225092
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|211437854|gb|FL220477.1|FL220477
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|78109883|gb|DV528299.1|DV528299
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|60341680|gb|DN208653.1|DN208653
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|88754483|gb|DY538624.1|DY538624
EST:     TAAACAAAAGAATTCAAGAAGCGTTCTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCCCCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|113702906|gb|EE680410.1|EE680410
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|60394174|gb|DN227044.1|DN227044
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|60359057|gb|DN226030.1|DN226030
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|6227143|gb|AW155672.1|AW155672
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|76926083|gb|DV170714.1|DV170714
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|93281145|gb|EB673409.1|EB673409
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGC-
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|6828185|gb|AW331828.1|AW331828
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|78021679|gb|DV490066.1|DV490066
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|93016890|gb|EB642410.1|EB642410
EST:     TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG                         GTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCC

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), 46 (downstream exon)
Score: 54

GTAAAACTTGTTAGGGTAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 72

GTAAAACTTGTTAGGGTAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

GTAAAACTTGTTAGGGTAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 47

GTAAAACTTGTTAGGGTAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGgtacaaatct ... tgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtgcaccattaaccttaataatattctaaagtagaaacctcctgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG
                          ttctaaa  putative branch site (score: 47)
                                        cctcctgc  putative PPT
          attaaccttaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaatctacctgtctaataagtaagagcaaattaatgcatttttagtgggtgcaccattaaccttaataatattctaaagtagaaacctcctgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT