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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaagacaccatctgctgttgtttagcattttgttttcaaaattatatccaattatttcgatgtcttgtttttgttatgttttatgcttcttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT

Basic information

species Zea mays
transcript GRMZM2G033526_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033526_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 9
gcaaagacaccatctgctgttgt-ttagcattttgttttcaaaattatatccaattatttcgatgtcttgtttttg-----ttatgtt-ttatgcttcttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT
            | |||| |||     ||  || |   ||||  |  | ||  |  | || | |  ||   ||||      |||| || | ||| ||||||||| ||| ||| |  || ||||| || || | |||||| ||||| |||||||| ||||||||||| || |||||||| ||||||||| |||| ||||| ||||| |
-----cttgtagtatgctattgcacctgctcttagacatcaagttcctttctta--agtttgttacctgaattttagcaccttattttctcatgattcttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT
















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|22133857|gb|BQ833942.1|BQ833942
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|60351363|gb|DN218336.1|DN218336
EST:     TCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: TCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|60355665|gb|DN222638.1|DN222638
EST:     TAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: TAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|166664767|gb|EG198258.1|EG198258
EST:     CTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTA-GTAAAATGTTCGGA
genomic: CTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|60355637|gb|DN222610.1|DN222610
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|32858382|gb|CD998063.1|CD998063
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|78180652|gb|DV550980.1|DV550980
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|22542067|gb|BU092505.1|BU092505
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|24765370|gb|CA400529.1|CA400529
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|60397119|gb|DN229938.1|DN229938
EST:     CAGCCTTTATAACCCAATTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|6973697|gb|AW438271.1|AW438271
EST:     CCAGCCTTTATAACCCANCTACTTCTCCTAGNCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|60338482|gb|DN205455.1|DN205455
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|12046501|gb|BF728640.1|BF728640
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGGCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGGTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|31357830|gb|CD442187.1|CD442187
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|87155458|gb|DY400247.1|DY400247
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|60356976|gb|DN223949.1|DN223949
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCT------                         -G-C-ACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|211275556|gb|FL192922.1|FL192922
EST:     AACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: AACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|67016939|gb|CO445688.1|CO445688
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|60395622|gb|DN228492.1|DN228492
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|76287860|gb|DV027428.1|DV027428
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA
EST: gi|67022089|gb|CO450838.1|CO450838
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         GGTCTACAGAATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGA

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: 252

TCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGAATCCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

TCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGAATCCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

TCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGAATCCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 495

TCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGAATCCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... cttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatccaattatttcgatgtcttgtttttgttatgttttatgcttcttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT
                                   ttttatgcttctttt  CT-rich tract
                        tttttgttatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaagacaccatctgctgttgtttagcattttgttttcaaaattatatccaattatttcgatgtcttgtttttgttatgttttatgcttcttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT

- - - -caccatc
- - - - - - - -gctgttg
- - - - - - - - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgctt