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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatctgctgttgtttagcattttgttttcaaaattatatccaattatttcgatgtcttgtttttgttatgttttatgcttcttttggcagggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA

Basic information

species Zea mays
transcript GRMZM2G033526_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 9
ccatctgctgttgtttagcattttgttttcaaaattatatccaatt----atttcgatgtcttgtttttg-----ttatgtt-ttatgcttcttttggcagggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA
 | | |  | |  | | |||  |  | ||  | || |  | |  ||    | || | |  ||   ||||      |||| || | ||| ||||||||| ||| ||| |  || ||||| || || | |||||| ||||| |||||||| ||||||||||| || |||||||| ||||||||| |||| ||||| ||||| |         
-cttgtagtatgctattgcacctgctcttagacatcaagttcctttcttaagtttgttacctgaattttagcaccttattttctcatgattcttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT---------
















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|211275556|gb|FL192922.1|FL192922
EST:     AACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGGGTCTACAG                 
genomic: AACCCAACTACTTCTCCTAGTCTTGTTGCATCT-------G-C-ACAGgtatgatcag ... gg
EST: gi|60395622|gb|DN228492.1|DN228492
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGGGTCTACAG                 
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCT-------G-C-ACAGgtatgatcag ... gg
EST: gi|60356976|gb|DN223949.1|DN223949
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         AATGAGGACTTCTCCGCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCA
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCA
EST: gi|31357830|gb|CD442187.1|CD442187
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGGGTCTACAG                 
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCT-------G-C-ACAGgtatgatcag ... gg
EST: gi|76287860|gb|DV027428.1|DV027428
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGGGTCTACAG                 
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCT-------G-C-ACAGgtatgatcag ... gg
EST: gi|60355637|gb|DN222610.1|DN222610
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGGGTCTACAG                 
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCT-------G-C-ACAGgtatgatcag ... gg
EST: gi|24765370|gb|CA400529.1|CA400529
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGGGTCTACAG                 
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCT-------G-C-ACAGgtatgatcag ... gg
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         G
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacag-
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         G
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacag-
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         G
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacag-
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         G
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacag-
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         G
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacag-
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAG                         G
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacag-
EST: gi|60397119|gb|DN229938.1|DN229938
EST:     CAGCCTTTATAACCCAATTACTTCTCCTAGTCTTGTTGCATCTGCACAGGGTCTACAG                 
genomic: CAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCT-------G-C-ACAGgtatgatcag ... gg
EST: gi|60338482|gb|DN205455.1|DN205455
EST:     CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGGGTCTACAG                 
genomic: CCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCT-------G-C-ACAGgtatgatcag ... gg

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: 44 (upstream exon), 48 (downstream exon)
Score: 14

TCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGAATCCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 11

TCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGAATCCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 17

TCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGAATCCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 42

TCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGAATCCAGCCTTTATAACCCAACTACTTCTCCTAGTCTTGTTGCATCTGCACAGgtatgatcag ... gggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcgatgtcttgtttttgttatgttttatgcttcttttggcagggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA
               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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatctgctgttgtttagcattttgttttcaaaattatatccaattatttcgatgtcttgtttttgttatgttttatgcttcttttggcagggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA

- - - gctgttg
- - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttttg