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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaatcccagtggtttttatagtatgccaaaaactttagcaggatagactggcttttctgatgggaaacaaccctttaacaaagaatcttacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG

Basic information

species Zea mays
transcript GRMZM5G830874_T04
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|20208417|gb|BQ134506.1|BQ134506
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|211046341|gb|FL092969.1|FL092969
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|78124910|gb|DV543294.1|DV543294
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|71418229|gb|DR804377.1|DR804377
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|78110728|gb|DV529126.1|DV529126
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|78543868|gb|DV621366.1|DV621366
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|60400536|gb|DN233343.1|DN233343
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|211376348|gb|FL146641.1|FL146641
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA

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), 47 (downstream exon)
Score: 113

CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 108

CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 163

CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagactggcttttctgatgggaaacaaccctttaacaaagaatcttacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG
                                         atcttac  putative branch site (score: 72)
                              tttaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaatcccagtggtttttatagtatgccaaaaactttagcaggatagactggcttttctgatgggaaacaaccctttaacaaagaatcttacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA