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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattagagcaaatggctcatttttgtgacagttctttttgatgctgtatgaaagcacaaactgttatttcatttccgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAGATGCAAGCTCAAGTTGCTCACAGTATTCAAACAAAATCACCTGCTTATA

Basic information

species Zea mays
transcript GRMZM2G018946_T02
intron # 6
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|78091533|gb|DV519907.1|DV519907
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|76915058|gb|DV165799.1|DV165799
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|78091532|gb|DV519906.1|DV519906
EST:     TTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|71442030|gb|DR823080.1|DR823080
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|93013550|gb|EB639070.1|EB639070
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|71435524|gb|DR816574.1|DR816574
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|91876766|gb|EB406723.1|EB406723
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|78088916|gb|DV517309.1|DV517309
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|31558428|gb|CD527640.1|CD527640
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|71419272|gb|DR804704.1|DR804704
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
EST: gi|71446837|gb|DR827887.1|DR827887
EST:     TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAG                         ATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG
genomic: TGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAG

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 2 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 28

GCCTGTTACCAATTTCAATGAAGTGGCGCTGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAGATGCAAGCTCAAGTTGCTCACAGTATTCAAACAAAATCACCTGCTTATA


Block sizes: 19 (upstream exon), 31 (downstream exon)
Score: 3

GCCTGTTACCAATTTCAATGAAGTGGCGCTGCACTTCATTGAGTGTATTTATTTGCATTTGGAAAATGTACGGCAAAAGgtgattagag ... cgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAGATGCAAGCTCAAGTTGCTCACAGTATTCAAACAAAATCACCTGCTTATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctttttgatgctgtatgaaagcacaaactgttatttcatttccgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAGATGCAAGCTCAAGTTGCTCACAGTATTCAAACAAAATCACCTGCTTATA
     ttttgat  putative branch site (score: 3)
                                    tttcatttccgtttt  putative PPT
                                 ttatttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattagagcaaatggctcatttttgtgacagttctttttgatgctgtatgaaagcacaaactgttatttcatttccgttttgaagATGCAAGGTCAATTCCCTCGCTCCATTCAAGCAAATGTGTCTACTTATGAGATGCAAGCTCAAGTTGCTCACAGTATTCAAACAAAATCACCTGCTTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA