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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaactacactgtggcggtgtgtggcaataacgaagaaatctgtgctgaatgtgaaaaattgaaatctattttaatgatcgtatggtttttggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCATGTTGTGGCCTCGGCTTAGGCTGGTGTCT

Basic information

species Zea mays
transcript GRMZM2G022453_T01
intron # 1
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|5761881|gb|AI966854.1|AI966854
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211510117|gb|FL332873.1|FL332873
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211367717|gb|FL344724.1|FL344724
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211222593|gb|FL333442.1|FL333442
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACC
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACC
EST: gi|211106942|gb|FL338699.1|FL338699
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211361992|gb|FL325584.1|FL325584
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGSTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211021435|gb|FL345703.1|FL345703
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|89248089|gb|DY619875.1|DY619875
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211349709|gb|FL339346.1|FL339346
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211317797|gb|FL309524.1|FL309524
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211325177|gb|FL364046.1|FL364046
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|60397723|gb|DN230539.1|DN230539
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|89248090|gb|DY619876.1|DY619876
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211269693|gb|FL318255.1|FL318255
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|149085931|gb|EE175459.2|EE175459
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|161589855|gb|EY962642.1|EY962642
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTG
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTG
EST: gi|211329266|gb|FL352876.1|FL352876
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211171825|gb|FL323733.1|FL323733
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211391286|gb|FL329725.1|FL329725
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|211432570|gb|FL331491.1|FL331491
EST:     GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTTCCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: GTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
EST: gi|110519086|gb|EE023673.1|EE023673
EST:     ACGTACTACGCCCAGGGGTACCAGGCCGTACCAG                         GCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT
genomic: ACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCAT

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: 44 (upstream exon), 48 (downstream exon)
Score: 55

GCCCCGCCTCCCGGGCTCGGCAGCGGCGGCTATCACAACCAGCAGCAGCCGTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCATGTTGTGGCCTCGGCTTAGGCTGGTGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

GCCCCGCCTCCCGGGCTCGGCAGCGGCGGCTATCACAACCAGCAGCAGCCGTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCATGTTGTGGCCTCGGCTTAGGCTGGTGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

GCCCCGCCTCCCGGGCTCGGCAGCGGCGGCTATCACAACCAGCAGCAGCCGTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCATGTTGTGGCCTCGGCTTAGGCTGGTGTCT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 75

GCCCCGCCTCCCGGGCTCGGCAGCGGCGGCTATCACAACCAGCAGCAGCCGTACGCGCCTGCGGAGACGTACTACGCCCAGGGGTACCAGGCCGTACCAGgtatgctgag ... ggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCATGTTGTGGCCTCGGCTTAGGCTGGTGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatgtgaaaaattgaaatctattttaatgatcgtatggtttttggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCATGTTGTGGCCTCGGCTTAGGCTGGTGTCT
                       ttttaat  putative branch site (score: 75)
                                               ttcctt  putative PPT
      tgaaaaattgaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaactacactgtggcggtgtgtggcaataacgaagaaatctgtgctgaatgtgaaaaattgaaatctattttaatgatcgtatggtttttggttccttagGCTATGGTCCTGTTGCTGAAGGAAGACCTGTGAGAATGAGGCGTCTCCCATGTTGTGGCCTCGGCTTAGGCTGGTGTCT

-aactaca
- - - - ctgtggc
- - - - - - - - - - - - - - - -gaagaaa
- - - - - - - - - - - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - gtgaaaaa