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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagtgtttgctattgcaagccgacttctccttcggtccttcccccctctataactagtgggaaagaaacgatggtaacagaccttattctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG

Basic information

species Zea mays
transcript GRMZM2G032267_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032267_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g62040.2 (Oryza sativa), 3'ss of exon 9
tgtagtgtttgctattgcaagccgacttctcc-ttcggtccttcccccctctataactagtgggaaagaaacgatggtaacagaccttattctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG
 |    |   | | || |   ||   |||    |||     |   |   | ||       | |  |   |   | |     | | |||        ||||| |||||||||||| ||||||||||||||||||| || |||||| | || ||||||||||||||  |||||
-gagtggaccggtcttaccttccagtttcagtgttctactataagcatttttaattgagattgctactgatgaacgactgtatatcttgaatctcttgcagGCATGCTATTCAGCTGCTATCACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG

upper sequence: GRMZM2G032267_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 10
--tgtagtgtttgctattgcaagccgacttctccttcggtccttcccccctctataactagtgggaaagaaacgatggtaacagaccttattctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG
  | ||   ||||   ||  |     |   |  |    |  | ||   |      | |||| |   | ||| |||| |||||| |  ||        || || ||||||||||||||||||||||| ||||| || || |||||| | || |||||||| |||||  |||||
attttaaattttgtagttttagttttataaccacca-agctcatcttactgaggcagctagcgaagatgaa-cgattgtaacacatgttgaatctcatgtagGCATGCTATTCAGTTGCTATCACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG
















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|32932061|gb|CF036873.1|CF036873
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|60342617|gb|DN209590.1|DN209590
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|4314889|gb|AI444686.2|AI444686
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|60351813|gb|DN218786.1|DN218786
EST:     CAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: CAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|4826086|gb|AI667714.1|AI667714
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|32842037|gb|CD981718.1|CD981718
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTG
EST: gi|21331671|gb|BQ487052.1|BQ487052
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|211496869|gb|FL295227.1|FL295227
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|60358619|gb|DN225592.1|DN225592
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|60347035|gb|DN214008.1|DN214008
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|22819003|gb|BU499093.1|BU499093
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|87157723|gb|DY402512.1|DY402512
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|26559755|gb|CA831990.1|CA831990
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|33096873|gb|CF056833.1|CF056833
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|5670860|gb|AI932123.1|AI932123
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|28983722|gb|BQ538786.2|BQ538786
EST:     ACAGCAGACATCTTTGAA                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: ACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|32840485|gb|CD980166.1|CD980166
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCC
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCC
EST: gi|60356915|gb|DN223888.1|DN223888
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|4321073|gb|AI467736.1|AI467736
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|67016264|gb|CO445013.1|CO445013
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|148952636|gb|EC898467.2|EC898467
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|32842224|gb|CD981905.1|CD981905
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATC
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATC
EST: gi|7162558|gb|AW520180.1|AW520180
EST:     TTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: TTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|7227451|gb|AW566092.1|AW566092
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
EST: gi|71420713|gb|DR805175.1|DR805175
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGG

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: 46 (upstream exon), 49 (downstream exon)
Score: 30

ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 11

ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 14

ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 19

ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctctataactagtgggaaagaaacgatggtaacagaccttattctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG
                            tggtaac  putative branch site (score: 19)
                                      ccttattctctctgc  putative PPT
     tataacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagtgtttgctattgcaagccgacttctccttcggtccttcccccctctataactagtgggaaagaaacgatggtaacagaccttattctctctgcagACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG