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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgctagtaaaatgcccaaatcctgtcttgatgtctttcttggttcatttgtttttaatgttgagctcttatttgagtagctacaatctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTA

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 8
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|67028781|gb|CO457530.1|CO457530
EST:     AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG                         GCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
genomic: AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
EST: gi|60349712|gb|DN216685.1|DN216685
EST:     AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG                         GCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
genomic: AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
EST: gi|13178345|gb|BG349603.1|BG349603
EST:     AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG                         GCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
genomic: AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
EST: gi|22543150|gb|BU093588.1|BU093588
EST:     AATTCATAGCTCTTTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG                         GCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
genomic: AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
EST: gi|22935539|gb|BU571814.1|BU571814
EST:     AATTCATAGCTCTTTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG                         GCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
genomic: AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
EST: gi|60342116|gb|DN209089.1|DN209089
EST:     AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG                         GCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
genomic: AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
EST: gi|32941898|gb|CF046717.1|CF046717
EST:     AATTCATAGCTCTTTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG                         GCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA
genomic: AATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTA

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: 103

GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 165

GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAGgtggtgctac ... ctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcatttgtttttaatgttgagctcttatttgagtagctacaatctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTA
                                           atctaat  putative branch site (score: 165)
     tttgtttttaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgctagtaaaatgcccaaatcctgtcttgatgtctttcttggttcatttgtttttaatgttgagctcttatttgagtagctacaatctaattttagGCGGAGAACGTCATTAAACAGCTTCAAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTA

-ttttgct
- - - - - - -aatgccc
- - - - - - - - - - - - - - - ttgatgt
- - - - - - - - - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctaca