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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccctccagagctcccccacccacccaccacacacacacacagtagttgtgcttaaacatctgtatttccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGGACGTTGAGAAGGGTTCGGAGTATGCTATCACATTCAGTGCTGCCCGGAC

Basic information

species Zea mays
transcript GRMZM2G324705_T01
intron # 2
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|9254221|gb|BE344689.1|BE344689
EST:     CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGG                         GGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
genomic: CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
EST: gi|31612031|gb|CD568653.1|CD568653
EST:     CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGG                         GGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
genomic: CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
EST: gi|9953009|gb|BE639592.1|BE639592
EST:     CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGG                         GGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
genomic: CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
EST: gi|22936026|gb|BU572301.1|BU572301
EST:     CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGG                         GGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
genomic: CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
EST: gi|9953202|gb|BE639785.1|BE639785
EST:     CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGG                         GGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG
genomic: CATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGG

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: 391

GAGGGTGCATCGTCAATCCCTGGTTGGACGATCAACGGCACGGTTGAACTCATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGGACGTTGAGAAGGGTTCGGAGTATGCTATCACATTCAGTGCTGCCCGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GAGGGTGCATCGTCAATCCCTGGTTGGACGATCAACGGCACGGTTGAACTCATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGGACGTTGAGAAGGGTTCGGAGTATGCTATCACATTCAGTGCTGCCCGGAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 36

GAGGGTGCATCGTCAATCCCTGGTTGGACGATCAACGGCACGGTTGAACTCATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGGACGTTGAGAAGGGTTCGGAGTATGCTATCACATTCAGTGCTGCCCGGAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 215

GAGGGTGCATCGTCAATCCCTGGTTGGACGATCAACGGCACGGTTGAACTCATTTCAGCAGGCCAACACCAGGGTGGCATGATCCTGATTGTTCCACAGGgtacccctcc ... tccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGGACGTTGAGAAGGGTTCGGAGTATGCTATCACATTCAGTGCTGCCCGGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccaccacacacacacacagtagttgtgcttaaacatctgtatttccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGGACGTTGAGAAGGGTTCGGAGTATGCTATCACATTCAGTGCTGCCCGGAC
                                         tatttcc  CT-rich tract
                              ttaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccctccagagctcccccacccacccaccacacacacacacagtagttgtgcttaaacatctgtatttccgtggcagGGGACCATGCAGTAAGGCTAGGGAATGATGCTAGCGTTGGGCAGGTGGTGGACGTTGAGAAGGGTTCGGAGTATGCTATCACATTCAGTGCTGCCCGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC