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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcgtacttccgtttccgaaccaaaattcacttttatttagataaccacaactgacgatgtttgcaaattggtttgcttgtcaactttacgttagttctgtttgtggagtttgggtattgaagctttgtatgtcttgttgggttcattttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGACCAATATG

Basic information

species Zea mays
transcript GRMZM2G147256_T02
intron # 4
splice site 3'
intron type U2

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|71299596|gb|DR785811.1|DR785811
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGACTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|76912287|gb|DV164658.1|DV164658
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|101397910|gb|EB820832.1|EB820832
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|149098292|gb|EE184260.2|EE184260
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|89763649|gb|DY690753.1|DY690753
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|94474055|gb|EB703013.1|EB703013
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATCACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|84970143|gb|DW468493.1|DW468493
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|78124407|gb|DV542791.1|DV542791
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|93284471|gb|EB676735.1|EB676735
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|74236569|gb|DT644483.1|DT644483
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|78119582|gb|DV537966.1|DV537966
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACGGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|50336979|gb|CO532105.1|CO532105
EST:     AGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: AGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|50335970|gb|CO531096.1|CO531096
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|60356954|gb|DN223927.1|DN223927
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|78124376|gb|DV542760.1|DV542760
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|71758972|gb|DR956909.1|DR956909
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
EST: gi|14245232|gb|BG873814.1|BG873814
EST:     CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAG                         AGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA
genomic: CACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGA

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: 44 (upstream exon), 48 (downstream exon)
Score: 36

ATGAGACAGGTGGGAGTTCTTTGTGCTGCTGCTCATGTTGCCGTTCGTGACACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGACCAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

ATGAGACAGGTGGGAGTTCTTTGTGCTGCTGCTCATGTTGCCGTTCGTGACACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGACCAATATG


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 27

ATGAGACAGGTGGGAGTTCTTTGTGCTGCTGCTCATGTTGCCGTTCGTGACACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGACCAATATG


Block sizes: 30 (upstream exon), 48 (downstream exon)
Score: 20

ATGAGACAGGTGGGAGTTCTTTGTGCTGCTGCTCATGTTGCCGTTCGTGACACTGTGGGAAAGCTTGCGGATGACCACAGGAAGGCTAAAGCTTTGGCAGgtttcgtact ... attttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGACCAATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtggagtttgggtattgaagctttgtatgtcttgttgggttcattttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGACCAATATG
                                          ttcattttctt  CT-rich tract
                                             attttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcgtacttccgtttccgaaccaaaattcacttttatttagataaccacaactgacgatgtttgcaaattggtttgcttgtcaactttacgttagttctgtttgtggagtttgggtattgaagctttgtatgtcttgttgggttcattttcttagAGGGACTGAAGAAAATCGAGCAGATTACAGTGGATTCAGCTTCGGTCGAGACCAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT