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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatggattaggatccaatcatttgcgtctctgttgagaacttagttacttgtatatgcaattaataactgtttgcacaaaataattgtttcttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAATCCTGACAACAGCTATCGTCAAATCTACGACATTCCCAGCAATGACTATG

Basic information

species Zea mays
transcript GRMZM2G019991_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|211314558|gb|FL124188.1|FL124188
EST:     TGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG                         GGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAAT
genomic: TGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAGgtgataggca ... cttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAAT
EST: gi|60338254|gb|DN205227.1|DN205227
EST:     TGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG                         GGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAAT
genomic: TGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAGgtgataggca ... cttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAAT
EST: gi|71432024|gb|DR813074.1|DR813074
EST:     TGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG                         GGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAAT
genomic: TGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAGgtgataggca ... cttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAAT
EST: gi|211314557|gb|FL124187.1|FL124187
EST:     TGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAG                         GGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAAT
genomic: TGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAGgtgataggca ... cttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 82

TTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAGgtgataggca ... cttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAATCCTGACAACAGCTATCGTCAAATCTACGACATTCCCAGCAATGACTATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 89

TTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAGgtgataggca ... cttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAATCCTGACAACAGCTATCGTCAAATCTACGACATTCCCAGCAATGACTATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 66

TTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAGgtgataggca ... cttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAATCCTGACAACAGCTATCGTCAAATCTACGACATTCCCAGCAATGACTATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 88

TTCCCTGATAATAAGGTGATGGATCAAGTGCATTTTGCCAACTCGCCACTTCAGCAACAGACAATTGATTTTTCAGAGgtgataggca ... cttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAATCCTGACAACAGCTATCGTCAAATCTACGACATTCCCAGCAATGACTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttgtatatgcaattaataactgtttgcacaaaataattgtttcttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAATCCTGACAACAGCTATCGTCAAATCTACGACATTCCCAGCAATGACTATG
                taataac  putative branch site (score: 88)
                                       ttgtttcttcctgc  putative PPT
      tatatgcaattaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatggattaggatccaatcatttgcgtctctgttgagaacttagttacttgtatatgcaattaataactgtttgcacaaaataattgtttcttcctgcagGGTAACAAACTGTTTGCTGAGAGAGGTCTGAGCAGTCCAGTGAAACTTAATCCTGACAACAGCTATCGTCAAATCTACGACATTCCCAGCAATGACTATG

- - - - - - - - - catttgc
- - - - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - - - ttacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa