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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggctagtttggcagccacaaaaccgcctcccaaactagccctcagtgtatatttgttcccttgctagcttccaccctattctgactggcttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAAAGGATCGAGCAGTCTTCACAATCTGTGAACGTGACTACTCCAGCACAAG

Basic information

species Zea mays
transcript GRMZM2G165755_T09
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|93013275|gb|EB638795.1|EB638795
EST:     GGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAG                         GCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
genomic: GGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
EST: gi|86470412|gb|DY236782.1|DY236782
EST:     CCCAGGACGCCGCTCCCGTGATTTTACGGCCATTGCAAAG                         GTTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
genomic: CCCAGGACGCCGCT-CCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
EST: gi|76910935|gb|DV164104.1|DV164104
EST:     CTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAG                         GCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
genomic: CTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
EST: gi|60397828|gb|DN230644.1|DN230644
EST:     CTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAG                         GCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
genomic: CTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
EST: gi|71418200|gb|DR804361.1|DR804361
EST:     CGGGATGGTCCCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAG                         GCTATTCAGAGAAGTCGTCCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
genomic: CTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
EST: gi|50334293|gb|CO529419.1|CO529419
EST:     CTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAG                         GCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA
genomic: CTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAA

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), 48 (downstream exon)
Score: 34

GCTGCCGGTTTGGGCGTTGAGGGTCACACCGACAAAGAGGAGCCCGCTTCCTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAAAGGATCGAGCAGTCTTCACAATCTGTGAACGTGACTACTCCAGCACAAG


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 7

GCTGCCGGTTTGGGCGTTGAGGGTCACACCGACAAAGAGGAGCCCGCTTCCTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAAAGGATCGAGCAGTCTTCACAATCTGTGAACGTGACTACTCCAGCACAAG


Block sizes: 32 (upstream exon), 27 (downstream exon)
Score: 8

GCTGCCGGTTTGGGCGTTGAGGGTCACACCGACAAAGAGGAGCCCGCTTCCTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAAAGGATCGAGCAGTCTTCACAATCTGTGAACGTGACTACTCCAGCACAAG


Block sizes: 40 (upstream exon), 10 (downstream exon)
Score: 2

GCTGCCGGTTTGGGCGTTGAGGGTCACACCGACAAAGAGGAGCCCGCTTCCTGGATGGTACCCCAGGACGCCGCTCCGTGATATTACGGCCATTGCAAAGgtgtgcatac ... ttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAAAGGATCGAGCAGTCTTCACAATCTGTGAACGTGACTACTCCAGCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtatatttgttcccttgctagcttccaccctattctgactggcttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAAAGGATCGAGCAGTCTTCACAATCTGTGAACGTGACTACTCCAGCACAAG
                                  ttctgac  putative branch site (score: 2)
                                            cttccat  putative PPT
     tatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggctagtttggcagccacaaaaccgcctcccaaactagccctcagtgtatatttgttcccttgctagcttccaccctattctgactggcttccatgcagGCTATTCAGAGAAGTCGTTCAAGGATTGCTGCAGCTCAGCAGCGAAGCCAAAGGATCGAGCAGTCTTCACAATCTGTGAACGTGACTACTCCAGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG