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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattagagcaaatggcaattttttgtgtcagttatattttgatgttgtatgaaaacacaagcagacaagctgttatttccttttcattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAGATGCAAGCTCAAGTCGCTCACACAGTTCAAACAAATGTGCCTGCTTATA

Basic information

species Zea mays
transcript GRMZM2G061485_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|71329934|gb|DR801689.1|DR801689
EST:     TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAG                         ATGAAGGATCATTTCCCTCGTGCTGTTCAAGCAAATGTGTCTG
genomic: TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTG
EST: gi|76280525|gb|DV020093.1|DV020093
EST:     TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAG                         ATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG
genomic: TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG
EST: gi|93017035|gb|EB642555.1|EB642555
EST:     TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAG                         ATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG
genomic: TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG
EST: gi|71321702|gb|DR797544.1|DR797544
EST:     TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAG                         ATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG
genomic: TGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAG

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: 40 (upstream exon), 39 (downstream exon)
Score: 10

GCCTGTTACTAATTTCAATGAATTGGCGCTGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAGATGCAAGCTCAAGTCGCTCACACAGTTCAAACAAATGTGCCTGCTTATA


Block sizes: 40 (upstream exon), 10 (downstream exon)
Score: 2

GCCTGTTACTAATTTCAATGAATTGGCGCTGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAGATGCAAGCTCAAGTCGCTCACACAGTTCAAACAAATGTGCCTGCTTATA


Block sizes: 40 (upstream exon), 10 (downstream exon)
Score: 1

GCCTGTTACTAATTTCAATGAATTGGCGCTGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAGATGCAAGCTCAAGTCGCTCACACAGTTCAAACAAATGTGCCTGCTTATA


Block sizes: 40 (upstream exon), 29 (downstream exon)
Score: 7

GCCTGTTACTAATTTCAATGAATTGGCGCTGCACTTCATTGAATGTATGTATGTGCATTTGGAAAATGTCCGGCCAAAGgtgattagag ... cattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAGATGCAAGCTCAAGTCGCTCACACAGTTCAAACAAATGTGCCTGCTTATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgttgtatgaaaacacaagcagacaagctgttatttccttttcattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAGATGCAAGCTCAAGTCGCTCACACAGTTCAAACAAATGTGCCTGCTTATA
 ttttgat  putative branch site (score: 7)
                              ctgttatttccttttc  putative PPT
                                         ttttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattagagcaaatggcaattttttgtgtcagttatattttgatgttgtatgaaaacacaagcagacaagctgttatttccttttcattttgaagATGAAGGATCAATTCCCTCGTGCTGTTCAAGCAAATGTGTCTGCTCACGAGATGCAAGCTCAAGTCGCTCACACAGTTCAAACAAATGTGCCTGCTTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA