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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagactcaatgctccatttccctccctacttctatctgcagcacatgttttgcaaggactagtgttagaaggaaatggagtcatcttctaacggg...

Basic information

species Zea mays
transcript GRMZM5G863152_T02
intron # 2
splice site 5'
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|211223994|gb|FL296362.1|FL296362
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211135925|gb|FL188995.1|FL188995
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211226060|gb|FL296376.1|FL296376
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAGAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAA-AGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|71305070|gb|DR788672.1|DR788672
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211226055|gb|FL296371.1|FL296371
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211223997|gb|FL296365.1|FL296365
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|76920373|gb|DV168136.1|DV168136
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211226059|gb|FL296375.1|FL296375
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211226058|gb|FL296374.1|FL296374
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211224000|gb|FL296368.1|FL296368
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|71432424|gb|DR813474.1|DR813474
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211223995|gb|FL296363.1|FL296363
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATCGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGAT-GTTGCACTGGAATCAAG
EST: gi|211226057|gb|FL296373.1|FL296373
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|78081578|gb|DV509990.1|DV509990
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
EST: gi|211223993|gb|FL296361.1|FL296361
EST:     TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAA                         ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG
genomic: TTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG

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), 44 (downstream exon)
Score: 126

TTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 183

TTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 69

TTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 109

TTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagac ... tttctcccagATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCAATGGGCGTGGCTTCAGTGCGGATTCTACCAATAAGAGAAAAgtatgtagactcaatgctccatttccctccctacttctatctgcagcacatgttttgcaaggactagtgttagaaggaaatggagtcatcttctaacggg

- - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaggaaa