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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCGCCGCCGCGCCGTACCGCCGGCCTCTCCACCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcgtacccgtctccgtcttttgcgtggcgcatgggttctgtatgtctcatcatgcgtcgcttgctcacccgcttggtcgcag

Basic information

species Zea mays
transcript GRMZM2G093902_T02
intron # 1
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|211411263|gb|FK965131.1|FK965131
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|74240382|gb|DT648296.1|DT648296
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|148973769|gb|EE024903.2|EE024903
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|211413802|gb|FK965136.1|FK965136
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|211411267|gb|FK965135.1|FK965135
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|211411264|gb|FK965132.1|FK965132
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCNG
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCC-G
EST: gi|91052942|gb|EB163360.1|EB163360
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|76013473|gb|DT940643.1|DT940643
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|211411261|gb|FK965129.1|FK965129
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|88757758|gb|DY541899.1|DY541899
EST:     CTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|78109693|gb|DV528109.1|DV528109
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|50339749|gb|CO534875.1|CO534875
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|60346506|gb|DN213479.1|DN213479
EST:     CTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|74244112|gb|DT652026.1|DT652026
EST:     CTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
EST: gi|78024902|gb|DV493289.1|DV493289
EST:     CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAG                         TTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC
genomic: CCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGC

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 1 RNA-Seqlibrary.


Block sizes: 17 (upstream exon), 49 (downstream exon)
Score: 4

CGCCGCCGCCGCGCCGTACCGCCGGCCTCTCCACCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcg ... ttggtcgcagTTCGTGGCGGATGGCGTGTTCTTCGCGGAGCTGAATGAGATGCTGACCCGCGAGCTCGCGGAGGATGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCGCCGCCGCGCCGTACCGCCGGCCTCTCCACCGTTCATTCTCCAATGGCGTCGACTCACGCAATCAGCAAGAAGCGGAAGgtatggctcgtacccgtctccgtcttttgcgtggcgcatgggttctgtatgtctcatcatgcgtcgcttgctcacccgcttggtcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC