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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcactagagtaaaataattattcatatctttttaatcaggaatttttattgtggttcttccatatttagctcagtagtgaagcttggttgtattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAAAACTAAAGGAATGGCAGAATAAAGAAATTCTGTTGAGGGCAACAGCATG

Basic information

species Zea mays
transcript GRMZM2G142502_T02
intron # 9
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|22546253|gb|BU098564.1|BU098564
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAAT
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAAT
EST: gi|71422750|gb|DR805821.1|DR805821
EST:     CCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: CCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|211191423|gb|FL472420.1|FL472420
EST:     ACAATGCACCATGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|110517035|gb|EE021622.1|EE021622
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|149014311|gb|EE043888.2|EE043888
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|71759152|gb|DR957089.1|DR957089
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|28361590|gb|CB239946.1|CB239946
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|149079391|gb|EE168366.2|EE168366
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTTTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|78081829|gb|DV510241.1|DV510241
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|87157166|gb|DY401955.1|DY401955
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|60353959|gb|DN220932.1|DN220932
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|28390376|gb|CB250185.1|CB250185
EST:     ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
EST: gi|211359371|gb|FL212472.1|FL212472
EST:     ACAATGCACCATGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAA                         GATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA
genomic: ACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAA

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: 283

ATCAGTTATTCAACCTGCTGCGATGCAGATTTGGCAGTGGATGAACATTTACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAAAACTAAAGGAATGGCAGAATAAAGAAATTCTGTTGAGGGCAACAGCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

ATCAGTTATTCAACCTGCTGCGATGCAGATTTGGCAGTGGATGAACATTTACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAAAACTAAAGGAATGGCAGAATAAAGAAATTCTGTTGAGGGCAACAGCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

ATCAGTTATTCAACCTGCTGCGATGCAGATTTGGCAGTGGATGAACATTTACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAAAACTAAAGGAATGGCAGAATAAAGAAATTCTGTTGAGGGCAACAGCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

ATCAGTTATTCAACCTGCTGCGATGCAGATTTGGCAGTGGATGAACATTTACAATGCACCACGTTTTCCAGTGAAGAAGCGACAGCCTTTCTTTCTCAAAgtaaacatct ... tattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAAAACTAAAGGAATGGCAGAATAAAGAAATTCTGTTGAGGGCAACAGCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtggttcttccatatttagctcagtagtgaagcttggttgtattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAAAACTAAAGGAATGGCAGAATAAAGAAATTCTGTTGAGGGCAACAGCATG
                                          ttgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcactagagtaaaataattattcatatctttttaatcaggaatttttattgtggttcttccatatttagctcagtagtgaagcttggttgtattttgcagGATGGAAAGAAGCAATAGCCGCCGATCACGTGAAACTTGTTGTGTCCTGAAAACTAAAGGAATGGCAGAATAAAGAAATTCTGTTGAGGGCAACAGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
gcactag
- - - - - aaaataa
- - - - - - - - - - ttcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaagct