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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatccttcattaacattttttattggttttatttaattaatttatatgcaaaacatttttattggttttatttacaattcaaagtaaaaatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTTGCTGCCTTTAATATAAATGACTCATCTCCTCCTGATCACTCTG

Basic information

species Zea mays
transcript GRMZM2G021270_T01
intron # 19
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|31350260|gb|CD434617.1|CD434617
EST:     AACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAG                         GCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTT
genomic: AACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTT
EST: gi|22491413|gb|BU051336.1|BU051336
EST:     AACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAG                         GCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTT
genomic: AACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTT
EST: gi|87153215|gb|DY398004.1|DY398004
EST:     AACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAG                         GCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTT
genomic: AACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTT
EST: gi|93284596|gb|EB676860.1|EB676860
EST:     CCAGTAGTTGCAAAGGGGGGAGCTCAACAGAAGAAAGCACCCAAAAAG                         GCTCCCGGGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTT
genomic: CCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTT
EST: gi|87157557|gb|DY402346.1|DY402346
EST:     AACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAG                         GCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTNGAA-GACCGTCT
genomic: AACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACT-GAAAGACCGTCT

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: 707

ACAATGCTGCTGAACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTTGCTGCCTTTAATATAAATGACTCATCTCCTCCTGATCACTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

ACAATGCTGCTGAACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTTGCTGCCTTTAATATAAATGACTCATCTCCTCCTGATCACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 41

ACAATGCTGCTGAACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTTGCTGCCTTTAATATAAATGACTCATCTCCTCCTGATCACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

ACAATGCTGCTGAACCAGTAGTCGCAAAGCGTGGAGCTCAACAGAAGAAAGCACCCAAAAAGgttagaatct ... aatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTTGCTGCCTTTAATATAAATGACTCATCTCCTCCTGATCACTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgcaaaacatttttattggttttatttacaattcaaagtaaaaatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTTGCTGCCTTTAATATAAATGACTCATCTCCTCCTGATCACTCTG
           atttttattggtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatccttcattaacattttttattggttttatttaattaatttatatgcaaaacatttttattggttttatttacaattcaaagtaaaaatctcacagGCTCCCGTGGACGAAGAGGAAGTTGATATGCCTTCACTGAAAGACCGTCTTGCTGCCTTTAATATAAATGACTCATCTCCTCCTGATCACTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC