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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcgaaacccatcattagttgacctccctgtcgccgtcatgaccagcagacgggaaatctcaccctttttttttcttggtttggatctctctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCCGACTGACCACCGACCGACGGCAGCAGGCCGAAGGGCGTGCGGTGGCAGC

Basic information

species Zea mays
transcript GRMZM2G156606_T01
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|78024447|gb|DV492834.1|DV492834
EST:     ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAG                         CAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
genomic: ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
EST: gi|5757233|gb|AI964520.1|AI964520
EST:     ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAG                         CAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
genomic: ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
EST: gi|6022001|gb|AW066929.1|AW066929
EST:     ATGCGNCCAGGAGCAGGTCCGAGGTGCGCGAGAAGAAGTGCCCCAAGAAG                         CAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
genomic: ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
EST: gi|94479883|gb|EB708841.1|EB708841
EST:     ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAG                         CAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
genomic: ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
EST: gi|60353906|gb|DN220879.1|DN220879
EST:     ACCAGGAGCAGGTACGAGGTGCGCGAGAAGAACTGCCCCAAGAAG                         CAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATGGACAGCGACTCC
genomic: ACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
EST: gi|71313145|gb|DR793103.1|DR793103
EST:     ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAG                         CAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC
genomic: ATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCC

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: 48 (upstream exon), 48 (downstream exon)
Score: 35

GCGATCTGTCCCGGGGTGTGGCTGACGGATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCCGACTGACCACCGACCGACGGCAGCAGGCCGAAGGGCGTGCGGTGGCAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 17

GCGATCTGTCCCGGGGTGTGGCTGACGGATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCCGACTGACCACCGACCGACGGCAGCAGGCCGAAGGGCGTGCGGTGGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 16

GCGATCTGTCCCGGGGTGTGGCTGACGGATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCCGACTGACCACCGACCGACGGCAGCAGGCCGAAGGGCGTGCGGTGGCAGC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 35

GCGATCTGTCCCGGGGTGTGGCTGACGGATGCGACCAGGAGCAGGTACGAGGTGCGCGAGAAGAAGTGCCCCAAGAAGgtactctctc ... ctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCCGACTGACCACCGACCGACGGCAGCAGGCCGAAGGGCGTGCGGTGGCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagacgggaaatctcaccctttttttttcttggtttggatctctctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCCGACTGACCACCGACCGACGGCAGCAGGCCGAAGGGCGTGCGGTGGCAGC
           atctcac  putative branch site (score: 35)
                                        tctctctttgt  putative PPT
                    tttttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcgaaacccatcattagttgacctccctgtcgccgtcatgaccagcagacgggaaatctcaccctttttttttcttggtttggatctctctttgtgcagCAACAGAAGCACCGGGGCCTCAAGGGCATGGAGAGCATCGACAGCGACTCCGACTGACCACCGACCGACGGCAGCAGGCCGAAGGGCGTGCGGTGGCAGC

- - - -cccatca
- - - - - - - - - - - - - -ctgtcgc
- - - - - - - - - - - - - - - - - - - - - ccagcag