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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttgttgttgttgttgttgttgttgttgaaggaaaaggatgatgacagcacattatttctctgtag

Basic information

species Zea mays
transcript GRMZM2G157034_T02
intron # 12
splice site 5'
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|211305745|gb|FK970548.1|FK970548
EST:     AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAG                         CTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGAT-CCACT
genomic: AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACT
EST: gi|111433430|gb|EE297747.1|EE297747
EST:     AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAG                         CTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
genomic: AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
EST: gi|148969157|gb|EE019898.2|EE019898
EST:     AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTTTACCAGATCAG                         CTGGTCTGCCGACAGTAGGCTTTTACTAAGTGGAAGCAAGGATTCCACTCT
genomic: AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
EST: gi|33095385|gb|CF055379.1|CF055379
EST:     AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAG                         CTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
genomic: AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
EST: gi|33092990|gb|CF052984.1|CF052984
EST:     AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAG                         CTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
genomic: AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
EST: gi|110202220|gb|EC884117.1|EC884117
EST:     AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAG                         CTGGTCTGCCGACAGTAGGCTTTTATTAAGTGGAAGCAAGGATTCCACTCT
genomic: AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
EST: gi|148960782|gb|EE011442.2|EE011442
EST:     AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAG                         CTGGTCTGCCGACAGTAGGCTTTTACTAAGTGGAAGCAAGGATTCCACTCT
genomic: AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
EST: gi|32928456|gb|CF033268.1|CF033268
EST:     AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAG                         CTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT
genomic: AAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCT

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: 96

CAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCTAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 113

CAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 138

CAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

CAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttg ... ttctctgtagCTGGTCTGCCGACAGTAGGCTTCTACTAAGTGGAAGCAAGGATTCCACTCTAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTGTTGCAGCATTCAGAGGGCACGTTGCAGATGTCTACCAGATCAGgtgagttttgttgttgttgttgttgttgttgttgaaggaaaaggatgatgacagcacattatttctctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA