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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtggcgatttttggaattatctagaggaccgagcatgtgggctattacctgatttttttggtgacgaattgatagttttgatttccctaatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGAGAAGTTGATGGGACCGGGGGCACACTGGAAGGTTGTGTGAGATCGCGAA

Basic information

species Zea mays
transcript GRMZM2G396856_T02
intron # 1
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|211044486|gb|FL363792.1|FL363792
EST:     CCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAG                         TGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGA
genomic: CCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAGgtgggtctcg ... aatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGA
EST: gi|211417218|gb|FL339022.1|FL339022
EST:     CCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAG                         TGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGA
genomic: CCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAGgtgggtctcg ... aatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGA
EST: gi|211284781|gb|FL315063.1|FL315063
EST:     CCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAG                         TGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGA
genomic: CCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAGgtgggtctcg ... aatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGA
EST: gi|211287518|gb|FL360428.1|FL360428
EST:     CCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAG                         TGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGA
genomic: CCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAGgtgggtctcg ... aatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 71

ACAGCAGCAGGCCGGAGGTCTCCTCCTTCTACGCATCCACTGAGTTCCTTCCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAGgtgggtctcg ... aatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGAGAAGTTGATGGGACCGGGGGCACACTGGAAGGTTGTGTGAGATCGCGAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 34

ACAGCAGCAGGCCGGAGGTCTCCTCCTTCTACGCATCCACTGAGTTCCTTCCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAGgtgggtctcg ... aatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGAGAAGTTGATGGGACCGGGGGCACACTGGAAGGTTGTGTGAGATCGCGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 14

ACAGCAGCAGGCCGGAGGTCTCCTCCTTCTACGCATCCACTGAGTTCCTTCCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAGgtgggtctcg ... aatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGAGAAGTTGATGGGACCGGGGGCACACTGGAAGGTTGTGTGAGATCGCGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 240

ACAGCAGCAGGCCGGAGGTCTCCTCCTTCTACGCATCCACTGAGTTCCTTCCTGCGCAAAGTAAATCCCCAGTTCTTTCGGCCGCTGCCAAGTTTTCGAGgtgggtctcg ... aatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGAGAAGTTGATGGGACCGGGGGCACACTGGAAGGTTGTGTGAGATCGCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacctgatttttttggtgacgaattgatagttttgatttccctaatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGAGAAGTTGATGGGACCGGGGGCACACTGGAAGGTTGTGTGAGATCGCGAA
                                         ccctaat  putative branch site (score: 240)
                                      tttcccta  CT-rich tract
      tgattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgtggcgatttttggaattatctagaggaccgagcatgtgggctattacctgatttttttggtgacgaattgatagttttgatttccctaatttcgcagTGTTGCTAGCCCCGCCAGAGTTTTCTTCTCCCCCGCAGTCGAATTGGGCGAGAAGTTGATGGGACCGGGGGCACACTGGAAGGTTGTGTGAGATCGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - gagcatg