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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtttttccaatttgaatgcttgactttacctagcatcttctgcgcatttaccttctccacagcatctactgattatacaaggtaattattttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACAAAAATCTCAACAAAACCTGGCAGCGGGACGGAGCCACAGACTGACCCGA

Basic information

species Zea mays
transcript GRMZM2G139837_T01
intron # 3
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|9743186|gb|BE519334.1|BE519334
EST:     CAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATG                         GTGCTCTCTGAGCTTGACAGTTCTGATGAACCATCTGTATCTAGTGGGACA
genomic: CAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACA
EST: gi|211289089|gb|FL445033.1|FL445033
EST:     GGGAGGGACAGATTTATCGTCGAC-TTGAGGGAAACCAGGATG                         GTGCTCTCTGAGCTTGACAGTTCTGATGAACCATCTGTATCTAGTGGGACA
genomic: GGGA-GGACAGATTTATCGTCGACTTTGA-GGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACA
EST: gi|60395009|gb|DN227878.1|DN227878
EST:     CAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATG                         GTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACA
genomic: CAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACA
EST: gi|5847079|gb|AW000158.1|AW000158
EST:     -AAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAAACCAGGATG                         GTGCTCTCTGAGCTTGACAGTTCTGATGAACCATCTGTATCTAGTGGGACA
genomic: AAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGG-AAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACA
EST: gi|78021560|gb|DV489947.1|DV489947
EST:     AAACAATGGGAGGACAGATTTATCGTCGAC-TTGAGGAAACCAGGATG                         GTGCTCTCTGAGCTTGACAGTTCTGATGAACCATCTGTATCTAGTGGGACA
genomic: AAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACA
EST: gi|76293831|gb|DV033399.1|DV033399
EST:     CAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATG                         GTGCTCTCTGAGCTTGACNATTCTGATGAACCATCTGTATCTAGTGG
genomic: CAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGG
EST: gi|71762456|gb|DR960393.1|DR960393
EST:     CAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATG                         GTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACA
genomic: CAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACA

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), 26 (downstream exon)
Score: 58

TATGCCAGAAATTCCGGATATACCAAAGTGCTTACCTGATTTGCGTGCGTCAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACAAAAATCTCAACAAAACCTGGCAGCGGGACGGAGCCACAGACTGACCCGA


Block sizes: 47 (upstream exon), 21 (downstream exon)
Score: 33

TATGCCAGAAATTCCGGATATACCAAAGTGCTTACCTGATTTGCGTGCGTCAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACAAAAATCTCAACAAAACCTGGCAGCGGGACGGAGCCACAGACTGACCCGA


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 45

TATGCCAGAAATTCCGGATATACCAAAGTGCTTACCTGATTTGCGTGCGTCAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACAAAAATCTCAACAAAACCTGGCAGCGGGACGGAGCCACAGACTGACCCGA


Block sizes: 47 (upstream exon), 22 (downstream exon)
Score: 55

TATGCCAGAAATTCCGGATATACCAAAGTGCTTACCTGATTTGCGTGCGTCAAAACAATGGGAGGACAGATTTATCGTCGACTTTGAGGAAACCAGGATGgtaagttatc ... ttttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACAAAAATCTCAACAAAACCTGGCAGCGGGACGGAGCCACAGACTGACCCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatttaccttctccacagcatctactgattatacaaggtaattattttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACAAAAATCTCAACAAAACCTGGCAGCGGGACGGAGCCACAGACTGACCCGA
                       tactgat  putative branch site (score: 55)
                                          ttattttcctc  putative PPT
                            attatacaaggtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgtttttccaatttgaatgcttgactttacctagcatcttctgcgcatttaccttctccacagcatctactgattatacaaggtaattattttcctcagGTGCTCTCTGAGCTTGACAATTCTGATGAACCATCTGTATCTAGTGGGACAAAAATCTCAACAAAACCTGGCAGCGGGACGGAGCCACAGACTGACCCGA

- - - - - - - tgaatgc
- - - - - - - - - - - - - - - - - - - cttctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatt