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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgaacagagtttgttttcttatgtatgtcttatctgcaacctaacactccaatctttcttgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG

Basic information

species Zea mays
transcript GRMZM2G003692_T07
intron # 6
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|14244326|gb|BG842296.2|BG842296
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|5343223|gb|AI795408.1|AI795408
EST:     AGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|14208321|gb|BG842006.1|BG842006
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|37397592|gb|CF636096.1|CF636096
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|149101270|gb|EE187382.2|EE187382
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|32856130|gb|CD995811.1|CD995811
EST:     AAACGGAGGGCTCTAGAAGAGAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|32840502|gb|CD980183.1|CD980183
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|40337101|gb|CK371171.1|CK371171
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|67023347|gb|CO452096.1|CO452096
EST:     GGCTCTANAANAAA-TGAGGGAA-GTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: GGCTCTAGAAGAAAGTGA-GGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|32864069|gb|CF003751.1|CF003751
EST:     TAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|71759817|gb|DR957754.1|DR957754
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|6095476|gb|AW120143.1|AW120143
EST:     GAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: GAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|6194694|gb|AW146798.1|AW146798
EST:     GAGGAAGGTCTTANG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: GAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|93015973|gb|EB641493.1|EB641493
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|37387558|gb|CF630976.1|CF630976
EST:     GAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: GAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|71438969|gb|DR820019.1|DR820019
EST:     AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA

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: 42 (upstream exon), 46 (downstream exon)
Score: 180

AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 369

AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 351

AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 404

AAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttatgtatgtcttatctgcaacctaacactccaatctttcttgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG
                        acctaac  putative branch site (score: 404)
                                ctccaatctttctt  CT-rich tract
     tatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgaacagagtttgttttcttatgtatgtcttatctgcaacctaacactccaatctttcttgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG