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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcagcaatatgtgttacaggacagaagtagtaaaaagtcagtgaattagtaatgttgtataagtaacatgtctgtcactcattacttcattttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAAGCAAAG

Basic information

species Zea mays
transcript GRMZM2G111510_T01
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|78088731|gb|DV517124.1|DV517124
EST:     GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAG                         ATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAA
genomic: GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAA
EST: gi|33095039|gb|CF055033.1|CF055033
EST:     GCATGGATGACTCGAACGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAG                         ATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAA
genomic: GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAA
EST: gi|166467448|gb|EG132360.1|EG132360
EST:     GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAG                         ATTCACTGCATGAGGGAGTTTGAAGAAGGTGCTGAAAAG
genomic: GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAG
EST: gi|71432126|gb|DR813176.1|DR813176
EST:     GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAG                         ATTCACTGCATGGGGGAGTTTGAAGAANGTGCTGAA
genomic: GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAA
EST: gi|28984330|gb|BQ538995.2|BQ538995
EST:     GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAG                         ATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAA
genomic: GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAA
EST: gi|32932991|gb|CF037803.1|CF037803
EST:     GCATGGATGACTCGAACGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAG                         ATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAA
genomic: GCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAA
EST: gi|166577478|gb|EG062415.1|EG062415
EST:     CTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAG                         ATTCACTGCATGGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGA
genomic: CTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCAT-GGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGA

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: 199

GCTCACAGCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAAGCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 31

GCTCACAGCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAAGCAAAG


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

GCTCACAGCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAAGCAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 39

GCTCACAGCATGGATGACTCGAATGAAGGTGCTGAAAAGGATCTGGAAGGAATAAAGgtgatcacat ... ttttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAAGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtaatgttgtataagtaacatgtctgtcactcattacttcattttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAAGCAAAG
                aagtaac  putative branch site (score: 39)
                                        cttcatttt  putative PPT
                                    attacttcattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcagcaatatgtgttacaggacagaagtagtaaaaagtcagtgaattagtaatgttgtataagtaacatgtctgtcactcattacttcattttatctagATTCACTGCATGGGGGAGTTTGAAGAAGGTGCTGAAAAGAACCTGGAAGAAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
-gcagcaa
- - - - - - - - - - - - - - - gtaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtct