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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccttccatgtgggtacgctcgactgaaatccaattatccaaacatgatgatatcttgccatgattgccttgacgcaattaattttctgcaacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGGAGTTGAGCTGGCACTCGAATTCTTTCATGCATTGTGAGCGCAGGATCTG

Basic information

species Zea mays
transcript GRMZM5G806257_T01
intron # 14
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|60356359|gb|DN223332.1|DN223332
EST:     CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCCTTTATTCAG                         TGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|91867732|gb|EB399773.1|EB399773
EST:     CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAG                         TGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|5525495|gb|AI861388.1|AI861388
EST:     CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAG                         TGGCTCAAGGAAGCTGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|8102881|gb|AW927559.1|AW927559
EST:     CTGATGAGTCTGATAAAGTCTTTGTTAAACAGTCAGAAGCCTTTATTCAG                         TGGCTCAAGGAAGCTGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|8102880|gb|AW927558.1|AW927558
EST:     CTGATGAGTCTGATAAAGTCTTTGTTAAACAGTCAGAAGCCTTTATTCAG                         TGGCTCAAGGAAGCTGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|5325105|gb|AI783296.1|AI783296
EST:     CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAG                         TGGCTCAAGGAAGCTGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|32933173|gb|CF037985.1|CF037985
EST:     CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGTGGCTTTTATTCAG                         TGGCTCAAGGAAGCTGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|118406765|gb|EH038213.1|EH038213
EST:     CTGATGAGTCTGATAAAGTCTTTGTTAAACAGTCAGAAGCCTTTATTCAG                         TGGCTCAAGGAAGCTGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|5804618|gb|AI979588.1|AI979588
EST:     CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAG                         TGGCTCAAGGAAGCTGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
EST: gi|5714177|gb|AI944162.1|AI944162
EST:     CTGATGAGTCTGATAAAGTTTTTGTTAACCAGTCAGAGGCTTTTATTCAG                         TGGCTCAAGGAAGCTGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG
genomic: CTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGG

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), 47 (downstream exon)
Score: 114

GGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGGAGTTGAGCTGGCACTCGAATTCTTTCATGCATTGTGAGCGCAGGATCTG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 108

GGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGGAGTTGAGCTGGCACTCGAATTCTTTCATGCATTGTGAGCGCAGGATCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 135

GGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGGAGTTGAGCTGGCACTCGAATTCTTTCATGCATTGTGAGCGCAGGATCTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 54

GGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTGTTAAACAGTCAGAGGCTTTTATTCAGgtatatatcc ... aacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGGAGTTGAGCTGGCACTCGAATTCTTTCATGCATTGTGAGCGCAGGATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgatatcttgccatgattgccttgacgcaattaattttctgcaacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGGAGTTGAGCTGGCACTCGAATTCTTTCATGCATTGTGAGCGCAGGATCTG
                               aattaat  putative branch site (score: 54)
                                               cttctc  putative PPT
                               aattaattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccttccatgtgggtacgctcgactgaaatccaattatccaaacatgatgatatcttgccatgattgccttgacgcaattaattttctgcaacttctcagTGGCTCAAGGAAGCGGAAGAGGAGGATGACGAAGAAGAGGAATAACCCTGGAGTTGAGCTGGCACTCGAATTCTTTCATGCATTGTGAGCGCAGGATCTG

- - - catgtgg
- - - - - - - - - - - - - - - - - - - ccaaaca
- - - - - - - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - cttgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc