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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataaacatttacaaaccaatataaatacttgccttgtgctaatatcacatgactgtctctatttattggtgaacag

Basic information

species Zea mays
transcript GRMZM2G017077_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017077_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 9
TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataaacattta---caaaccaatataaatacttgccttgtgctaatatcacatgactgtctctatttattggtgaacag
||||||| ||||| |||||||||||||||||||| ||||| |||||||||||| | ||||||||||||||  | |   | |     |||      |  |||        ||  | | || |  |||  ||   |||||||| ||| ||||
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttgacattgtggactaaattttcgtggatatcactgaggtaattagatgatctgatcgttgttatttatttgtgcacag

upper sequence: GRMZM2G017077_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv05s0094g00150.t01 (Vitis vinifera), 5'ss of exon 8
TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataaacatttacaaaccaatataaatacttgccttgtgctaatatcacatgactgtctct-atttattggtgaacag------------------------
|  || | ||||| ||||||||||||||||| ||||||||| |  |||||||  | || |||||||||    | | |  |    |  |  |||       |   ||||   ||||| |    |   ||||  |  ||||    ||                           
TGTTGACAATGGAGTCCCAAGCAGAGGCACTGGGCCAGTTAACTTCTGATGAGCTTGACGGAAAGgtagctgttatctctctttactccttat-------tcttttgtctcaatattaagaaatgatctcccaagtattaaaaaaataaaatgaaataaaacaaaaaaggca
















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|60672345|gb|DN475106.1|DN475106
EST:     CCCAAGCAGAGGCACTTGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|16380324|gb|BI993429.1|BI993429
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|211105622|gb|FL311199.1|FL311199
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|148944166|gb|EC889255.2|EC889255
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|71759296|gb|DR957233.1|DR957233
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|5670871|gb|AI932134.1|AI932134
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|32841306|gb|CD980987.1|CD980987
EST:     CCCAAGCAGAGGCACTTGGCCAGTTAGCAACTGACGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|32841313|gb|CD980994.1|CD980994
EST:     CCCAAGCAGAGGCACTTGGCCAGTTAGCAACTGACGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|32841119|gb|CD980800.1|CD980800
EST:     CCCAAGCAGAGGCACTTGGCCAGTTAGCAACTGACGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|32841462|gb|CD981143.1|CD981143
EST:     CCCAAGCAGAGGCACTTGGCCAGTTAGCAACTGACGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|5670879|gb|AI932142.1|AI932142
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|88749527|gb|DY533668.1|DY533668
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|32840773|gb|CD980454.1|CD980454
EST:     CCCAAGCAGAGGCACTTGGCCAGTTAGCAACTGACGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|5607857|gb|AI901524.1|AI901524
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|32840756|gb|CD980437.1|CD980437
EST:     CCCAAGCAGAGGCACTTGGCCAGTTAGCAACTGACGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|6539065|gb|AW225204.1|AW225204
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|76019378|gb|DT946548.1|DT946548
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|76932094|gb|DV172939.1|DV172939
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|148950083|gb|EC895617.2|EC895617
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|18178217|gb|BM379427.1|BM379427
EST:     AGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: AGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|71770829|gb|DR968766.1|DR968766
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|12968090|gb|BG265037.1|BG265037
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
EST: gi|13198259|gb|BG354232.1|BG354232
EST:     CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAG                         TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA
genomic: CCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAA

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: 111

TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAAAAGGAATTGTCTGGAAGCTCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAAAAGGAATTGTCTGGAAGCTCTTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAAAAGGAATTGTCTGGAAGCTCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataa ... tggtgaacagTTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAAAAGGAATTGTCTGGAAGCTCTTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataaacatttacaaaccaatataaatacttgccttgtgctaatatcacatgactgtctctatttattggtgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA