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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccattgcactgcaaaatcctttactccttgccgatttaagtagtgcatggtggagtgatcaaatatatcagagcatcttttgcctcttcccccagtttttgtcgcacatccctgacagttctgtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTTGAGATGTCAGCAAGATTGATGGTTGCTAACAATGACCTTGTGCTGTTTC

Basic information

species Zea mays
transcript GRMZM2G140328_T02
intron # 32
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|74052474|gb|DN591091.1|DN591091
EST:     ATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAG                         CCCCTGATGACGCAACCTCTAATGATAAGGAAGACATCAAGCCCGAGCCTT
genomic: ATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAGgtagccattg ... gtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTT
EST: gi|32938257|gb|CF043076.1|CF043076
EST:     ATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAG                         CCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTT
genomic: ATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAGgtagccattg ... gtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTT
EST: gi|16925064|gb|BM078132.1|BM078132
EST:     ATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAG                         CCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTT
genomic: ATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAGgtagccattg ... gtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTT

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), 47 (downstream exon)
Score: 118

CTGGCCGCTGGCATTCGTGGGGAAGCTTATTCCTGTTCCTAAACGTCCATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAGgtagccattg ... gtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTTGAGATGTCAGCAAGATTGATGGTTGCTAACAATGACCTTGTGCTGTTTC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 15

CTGGCCGCTGGCATTCGTGGGGAAGCTTATTCCTGTTCCTAAACGTCCATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAGgtagccattg ... gtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTTGAGATGTCAGCAAGATTGATGGTTGCTAACAATGACCTTGTGCTGTTTC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 14

CTGGCCGCTGGCATTCGTGGGGAAGCTTATTCCTGTTCCTAAACGTCCATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAGgtagccattg ... gtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTTGAGATGTCAGCAAGATTGATGGTTGCTAACAATGACCTTGTGCTGTTTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 55

CTGGCCGCTGGCATTCGTGGGGAAGCTTATTCCTGTTCCTAAACGTCCATTGGGAGAATTCTTTGCATGCTGCTGTATCTGCAAGGGGAGCAAACAAGgtagccattg ... gtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTTGAGATGTCAGCAAGATTGATGGTTGCTAACAATGACCTTGTGCTGTTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcctcttcccccagtttttgtcgcacatccctgacagttctgtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTTGAGATGTCAGCAAGATTGATGGTTGCTAACAATGACCTTGTGCTGTTTC
                                ccctgac  putative branch site (score: 55)
                                         ttctgttt  putative PPT
                agttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagccattgcactgcaaaatcctttactccttgccgatttaagtagtgcatggtggagtgatcaaatatatcagagcatcttttgcctcttcccccagtttttgtcgcacatccctgacagttctgtttgtgcagCCCCTGATGACGCAACCTCTAATGATAAGGAAGACAACAAGCCCGAGCCTTGAGATGTCAGCAAGATTGATGGTTGCTAACAATGACCTTGTGCTGTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT