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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattatatgttctctttacagttaccattcagtttccagttttttaaggtgttctataactatttctctctatctatgatacaatattttgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG

Basic information

species Zea mays
transcript GRMZM2G009940_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009940_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 4
----tgattatatgttctctttacagttaccattcagtttccagttttttaaggtgttctataactatttctctctatctatgatacaatattttgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG
    |  | |||   |   | |||  ||   |   |  ||  |  ||| ||   ||| | |||  | ||  | | |||  |   ||  ||  || || |||||||| ||   ||||||||||||||||||||||||||||||||| || || |||||||||||||||||  ||||||||||||||||||
gatattttgataaaatagttgtacttttctgaaataaattttaaatttgtaca-tgtcccatagtt-ttgttttgtattgac--tatcatcattggtttaacagGATGAGGGTGTCAACATAACTGCAAATTCTCTTCATCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG
















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|211301865|gb|FL439779.1|FL439779
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|76280839|gb|DV020407.1|DV020407
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|32165056|gb|CD670374.1|CD670374
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|60347345|gb|DN214318.1|DN214318
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|78078135|gb|DV506550.1|DV506550
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|18168960|gb|BM338800.1|BM338800
EST:     AGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: AGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|78106300|gb|DV524718.1|DV524718
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|211543309|gb|FL433009.1|FL433009
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|91875958|gb|EB405915.1|EB405915
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|78106299|gb|DV524717.1|DV524717
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|67015441|gb|CO444190.1|CO444190
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|9733746|gb|BE512498.1|BE512498
EST:     GCAAACATATTGCATGCTAATGAACCTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: GCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|76280838|gb|DV020406.1|DV020406
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|5058970|gb|AI737446.1|AI737446
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|17931680|gb|BM268640.1|BM268640
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|149082933|gb|EE172168.2|EE172168
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|71438305|gb|DR819355.1|DR819355
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|78023811|gb|DV492198.1|DV492198
EST:     TTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: TTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|94475917|gb|EB704875.1|EB704875
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|74244969|gb|DT652883.1|DT652883
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|71317601|gb|DR795544.1|DR795544
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|18650256|gb|BM499075.1|BM499075
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|13249759|gb|BG360664.1|BG360664
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|60343084|gb|DN210057.1|DN210057
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|12969391|gb|BG266335.1|BG266335
EST:     CAGGCGATTTGAG                         GAAGATAATGTCAACATAGCTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
EST: gi|78105169|gb|DV523587.1|DV523587
EST:     CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG                         GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC
genomic: CAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATC

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: 171

GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAGgtatgtcttg ... tgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaggtgttctataactatttctctctatctatgatacaatattttgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG
         ctataac  putative branch site (score: 80)
                                          ttttgtct  putative PPT
                              tatgatacaatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattatatgttctctttacagttaccattcagtttccagttttttaaggtgttctataactatttctctctatctatgatacaatattttgtctaacagGAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATG

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