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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttttcttgtaccacactagatataattcatgaaatctgctcgtgggatagactttactgatatgcttgccactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGAGGCATGGTTTGCTGCAGATGCAGATGAAATATCTCTGAAGAACTGGGAT

Basic information

species Zea mays
transcript GRMZM2G078033_T01
intron # 6
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|14190990|gb|BG833220.1|BG833220
EST:     GGCACCCCCATCTAAA                         GCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
genomic: GGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
EST: gi|19350869|gb|BM895401.1|BM895401
EST:     CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA                         GCTTGAAGGGCTAGATGATCAGGACTTACAATGGTGTGTCTGCCGGCTTGA
genomic: CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
EST: gi|67029948|gb|CO458697.1|CO458697
EST:     CTACAGGC-ATTTCCTATTGTGTTTGAGAGGCACCCCCATCTAAA                         GCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
genomic: CTACAGGCAATTT-CTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
EST: gi|67021466|gb|CO450215.1|CO450215
EST:     CCACTGCTACTGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA                         GCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
genomic: CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
EST: gi|149011847|gb|EE042454.2|EE042454
EST:     CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA                         GCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
genomic: CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
EST: gi|31364427|gb|CD448782.1|CD448782
EST:     CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA                         GCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
genomic: CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
EST: gi|14190983|gb|BG833213.1|BG833213
EST:     GGCACCCCCATCTAAA                         GCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
genomic: GGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
EST: gi|67012438|gb|CO441187.1|CO441187
EST:     CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA                         GCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA
genomic: CCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGA

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: 138

ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGAGGCATGGTTTGCTGCAGATGCAGATGAAATATCTCTGAAGAACTGGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 317

ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGAGGCATGGTTTGCTGCAGATGCAGATGAAATATCTCTGAAGAACTGGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGAGGCATGGTTTGCTGCAGATGCAGATGAAATATCTCTGAAGAACTGGGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 212

ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAAgtattttttt ... cactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGAGGCATGGTTTGCTGCAGATGCAGATGAAATATCTCTGAAGAACTGGGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcatgaaatctgctcgtgggatagactttactgatatgcttgccactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGAGGCATGGTTTGCTGCAGATGCAGATGAAATATCTCTGAAGAACTGGGAT
                              tactgat  putative branch site (score: 212)
                                            ccacttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttttcttgtaccacactagatataattcatgaaatctgctcgtgggatagactttactgatatgcttgccactttgtagGCTTGAAGGGCTAGATGATCAGGTCTTACAATGGTGTGTCTGCCGGCTTGAGGCATGGTTTGCTGCAGATGCAGATGAAATATCTCTGAAGAACTGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC