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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaatactcaaatcgattcttgtaaacttgtattaaaggcaatattaatctataccatgttccattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAACCTCCACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCA

Basic information

species Zea mays
transcript GRMZM2G156638_T02
intron # 12
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|84976584|gb|DW475006.1|DW475006
EST:     TCACCTTCATCAAGCACTTTGATCCTGCTAATTGGGACCCTAATTATTAG                         TGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAG
genomic: TCACCTTCATCA-GCACTT-GATCCTGCTAATTGGGACCCTAATTAT-AGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAG
EST: gi|16925759|gb|BM078827.1|BM078827
EST:     TAATTGGGACCNTAATTATAG                         TGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
genomic: TAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
EST: gi|113703304|gb|EE680808.1|EE680808
EST:     TTTTCACCTTCATCAGCACTTGATCCTGTTAATTGGGACCCTAATTATAG                         TGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
genomic: TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
EST: gi|33098634|gb|CF058594.1|CF058594
EST:     TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAG                         TGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
genomic: TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
EST: gi|9732795|gb|BE511547.1|BE511547
EST:     TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAG                         TGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
genomic: TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
EST: gi|28986772|gb|CB351302.1|CB351302
EST:     TGCTAATTGGGACCCTAATTATAG                         TGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
genomic: TGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
EST: gi|14204013|gb|BG837690.1|BG837690
EST:     TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAG                         TGATGAGTCACTACTGCAAGACAATTCACTGTCAGCTGAACTAAGTAGCAA
genomic: TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
EST: gi|71758986|gb|DR956923.1|DR956923
EST:     CATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAG                         TGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
genomic: CATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA
EST: gi|33099099|gb|CF059059.1|CF059059
EST:     TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAG                         TGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAN
genomic: TTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 126

AGGCCTCGTCTAGTCATGTGCTTTCACAGGCTCCATCACAATCGTTTGACTTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAACCTCCACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

AGGCCTCGTCTAGTCATGTGCTTTCACAGGCTCCATCACAATCGTTTGACTTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAACCTCCACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 201

AGGCCTCGTCTAGTCATGTGCTTTCACAGGCTCCATCACAATCGTTTGACTTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAACCTCCACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 101

AGGCCTCGTCTAGTCATGTGCTTTCACAGGCTCCATCACAATCGTTTGACTTTTCACCTTCATCAGCACTTGATCCTGCTAATTGGGACCCTAATTATAGgtatggaata ... cattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAACCTCCACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtaaacttgtattaaaggcaatattaatctataccatgttccattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAACCTCCACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCA
                         tattaat  putative branch site (score: 101)
                                          ttccatttt  putative PPT
                       aatattaatctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaatactcaaatcgattcttgtaaacttgtattaaaggcaatattaatctataccatgttccattttgtagTGATGAGTCACTACTGCAGGACAATTCACTGTCAGCTGAACTAAGTAGCAACCTCCACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA